Where Science and Faith Converge
  • No Joke: New Pseudogene Function Smiles on the Case for Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Apr 01, 2020

    Time to confess. I now consider myself an evolutionary creationist. I have no choice. The evidence for biological evolution is so overwhelming…

    …Just kidding! April Fool’s!

    I am still an old-earth creationist. Even though the evolutionary paradigm is the prevailing framework in biology, I am skeptical about facets of it. I am more convinced than ever that a creation model approach is the best way to view life’s origin, design, and history. It’s not to say that there isn’t evidence for common descent; there is. Still, even with this evidence, I prefer old-earth creationism for three reasons.

    • First, a creation model approach can readily accommodate the evidence for common descent within a design framework.
    • Second, the evolutionary paradigm struggles to adequately explain many of the key transitions in life’s history.
    • Third, the impression of design in biology is overwhelming—and it’s becoming more so every day.

    And that is no joke.

    Take the human genome as an example. When it comes to understanding its structure and function, we are in our infancy. As we grow in our knowledge and insight, it becomes increasingly apparent that the structural and functional features of the human genome (and the genomes of other organisms) display more elegance and sophistication than most life scientists could have ever imagined—at least, those operating within the evolutionary framework. On the other hand, the elegance and sophistication of genomes is expected for creationists and intelligent design advocates. To put it simply, the more we learn about the human genome, the more it appears to be the product of a Mind.

    In fact, the advances in genomics over the last decade have forced life scientists to radically alter their views of genome biology. When the human genome was first sequenced in 2000, biologists considered most of the sequence elements to be nonfunctional, useless DNA. Now biologists recognize that virtually every class of these so-called junk DNA sequences serve key functional roles.

    If most of the DNA sequence elements in the human genome were truly junk, then I’d agree that it makes sense to view them as evolutionary leftovers, especially because these junk DNA sequences appear in corresponding locations of the human and primate genomes. It is for these reasons that biologists have traditionally interpreted these shared sequences as the most convincing evidence for common descent.

    However, now that we have learned that these sequences are functional, I think it is reasonable to regard them as the handiwork of a Creator, intentionally designed to contribute to the genome’s biology. In this framework, the shared DNA sequences in the human and primate genomes reflect common design, not common descent.

    Still, many biologists reject the common design interpretation, while continuing to express confidence in the evolutionary model. Their certainty reflects a commitment to methodological naturalism, but there is another reason for their confidence. They argue that the human genome (and the genomes of other organisms) display other architectural and operational features that the evolutionary framework explains best—and, in their view, these features tip the scales toward the evolutionary interpretation.

    Yet, researchers continue to make discoveries about junk DNA that counterbalance the evidence for common descent, including these structural and functional features. Recent insights into pseudogene biology nicely illustrate this trend.

    Pseudogenes

    Most life scientists view pseudogenes as the remnants of once-functional genes. Along these lines, biologists have identified three categories of pseudogenes (unitary, duplicated, and processed) and proposed three distinct mechanisms to explain the origin of each class. These mechanisms produce distinguishing features that allow investigators to identify certain DNA sequences as pseudogenes. However, a pre-commitment to the evolutionary paradigm can influence many biologists to declare too quickly that pseudogenes are nonfunctional based on their sequence characteristics.1

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    The Mechanisms of Pseudogene Formation. Image credit: Wikipedia.

    As the old adage goes: theories guide, experiments decide. There is an accumulation of experimental data which indicates that pseudogenes from all three classes have utility.

    A number of research teams have demonstrated that the cell’s machinery transcribes processed pseudogenes and, in turn, these transcripts are translated into proteins. Both duplicated and unitary pseudogenes are also transcribed. However, except for a few rare cases, these transcripts are not translated into proteins. Most of duplicated and unitary pseudogene transcripts serve a regulatory role, described by the competitive endogenous RNA hypothesis.

    In other words, the experimental support for pseudogene function seemingly hinges on the transcription of these sequences. That leads to the question: What about pseudogene sequences located in genomes that aren’t transcribed? A number of pseudogenic sequences in genomes seemingly sit dormant. They aren’t transcribed and, presumably, have no utility whatsoever.

    For many life scientists, this supports the evolutionary account for pseudogene origins, making it the preferred explanation over any model that posits the intentional design of pseudogene sequences. After all, why would a Creator introduce mutationally damaged genes that serve no function? Isn’t it better to explain the presence of functional processed pseudogenes as the result of neofunctionalization, whereby evolutionary mechanisms co-opt processed pseudogenes and use them as the raw material to evolve DNA sequence elements into new genes?

    Or, perhaps, is it better to view the transcripts of regulatory unitary and duplicated pseudogenes as the functional remnants of the original genes whose transcripts played a role in regulatory networks with other RNA transcripts? Even though these pseudogenes no longer direct protein production, they can still take part in the regulatory networks comprised of RNA transcripts.

    Are Untranscribed Pseudogenes Really Untranscribed?

    Again, remember that support for the evolutionary interpretation of pseudogenes rests on the belief that some pseudogenes are not transcribed. What happens to this support if these DNA sequences are transcribed, meaning we simply haven’t detected or identified their transcripts experimentally?

    As a case in point, in a piece for Nature Reviews, a team of collaborators from Australia argue that failure to detect pseudogene transcripts experimentally does not confirm the absence of a transcription.2 For example, the transcripts for a pseudogene transcribed at a low level may fall below the experimental detection limit. This particular pseudogene would appear inactive to researchers when, in fact, the opposite is the case. Additionally, pseudogene expression may be tissue-specific or may take place at certain points in the growth and development process. If the assay doesn’t take these possibilities into account, then failure to detect pseudogene transcripts could just mean that the experimental protocol is flawed.

    The similarity of the DNA sequences of pseudogenes and their corresponding “sister” genes causes another complication. It can be hard to experimentally distinguish between a pseudogene and its “intact” sister gene. This limitation means that, in some instances, pseudogene transcripts may be misidentified as the transcripts of the “intact” gene. Again, this can lead researchers to conclude mistakenly that the pseudogene isn’t transcribed.

    Are Untranscribed Pseudogenes Really Nonfunctional?

    These very real experimental challenges notwithstanding, there are pseudogenes that indeed are not transcribed, but it would be wrong to conclude that they have no role in gene regulation. For example, a large team of international collaborators demonstrated that a pseudogene sequence contributes to the specific three-dimensional architecture of chromosomes. By doing so, this sequence exerts influence over gene expression, albeit indirectly.3

    Another research team determined that a different pseudogene plays a role in maintaining chromosomal stability. In laboratory experiments, they discovered that deleting the DNA region that harbors this pseudogene increases chromosomal recombination events that result in the deletion of pieces of DNA. This deletion is catastrophic and leads to DiGeorge/velocardiofacial syndrome.4

    To be clear, these two studies focused on single pseudogenes. We need to be careful about extrapolating the results to all untranscribed pseudogenes. Nevertheless, at minimum, these findings open up the possibility that other untranscribed pseudogene sequences function in the same way. If past history is anything to go by when it comes to junk DNA, these two discoveries are most likely harbingers of what is to come. Simply put, we continue to uncover unexpected function for pseudogenes (and other classes of junk DNA).

    Common Design or Common Descent?

    Not that long ago, shared nonfunctional, junk DNA sequences in the human and primate genomes were taken as prima facia evidence for our shared evolutionary history with the great apes. There was no way to genuinely respond to the challenge junk DNA posed to creation models, other than to express the belief that we would one day discover function for junk DNA sequences.

    Subsequently, discoveries have fulfilled a key scientific prediction made by creationists and intelligent design proponents alike. These initial discoveries involved single, isolated pseudogenes. Later studies demonstrated that pseudogene function is pervasive, leading to new scientific ideas such as the competitive endogenous RNA hypothesis, that connect the sequence similarity of pseudogenes and “intact” genes to pseudogene function. Researchers are beginning to identify functional roles for untranscribed pseudogenes. I predict that it is only a matter of time before biologists concede that the utility of untranscribed pseudogenes is pervasive and commonplace.

    The creation model interpretation of shared junk DNA sequences becomes stronger and stronger with each step forward, which leads me to ask, When are life scientists going to stop fooling around and give a creation model approach a seat at the biology table?

    Resources

    Endnotes
    1. Seth W. Cheetham, Geoffrey J. Faulkner, and Marcel E. Dinger, “Overcoming Challenges and Dogmas to Understand the Functions of Pseudogenes,” Nature Reviews Genetics 21 (December 17, 2019): 191–201, doi:10.1038/s41576-019-0196-1.
    2. Cheetham et al., 191–201.
    3. Peng Huang, et al., “Comparative Analysis of Three-Dimensional Chromosomal Architecture Identifies a Novel Fetal Hemoglobin Regulatory Element,” Genes and Development 31, no. 16 (August 15, 2017): 1704–13, doi: 10.1101/gad.303461.117.
    4. Laia Vergés et al., “An Exploratory Study of Predisposing Genetic Factors for DiGeorge/Velocardiofacial Syndrome,” Scientific Reports 7 (January 6, 2017): id. 40031, doi: 10.1038/srep40031.
  • Does Evolutionary Bias Create Unhealthy Stereotypes about Pseudogenes?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Mar 18, 2020

    Truth be told, we all hold to certain stereotypes whether we want to admit it or not. Though unfair, more often than not, these stereotypes cause little real damage.

    Yet, there are instances when stereotypes can be harmful—even deadly. As a case in point, researchers have shown that stereotyping disrupts the healthcare received by members of so-called disadvantaged groups, such as African Americans, Latinos, and the poor.1

    Healthcare providers are frequently guilty of bias towards underprivileged people. Often, the stereotyping is unconscious and unintentional. Still, this bias compromises the medical care received by people in these ethnic and socioeconomic groups.

    Underprivileged patients are also guilty of stereotyping. It is not uncommon for these patients to perceive themselves as the victims of prejudice, even when their healthcare providers are genuinely unbiased. As a result, these patients don’t trust healthcare workers and, consequently, withhold information that is vital for a proper diagnosis.

    Fortunately, psychologists have developed best practices that can reduce stereotyping by both healthcare practitioners and patients. Hopefully, by implementing these practices, the impact of stereotyping on the quality of healthcare can be minimized over time.

    Recently, a research team from Australia identified another form of stereotyping that holds the potential to negatively impact healthcare outcomes.2 In this case, the impact of this stereotyping isn’t limited to disadvantaged people; it affects all of us.

    A Bias Against Pseudogenes

    These researchers have uncovered a bias in the way life scientists view the human genome (and the genomes of other organisms). Too often they regard the human genome as a repository of useless, nonfunctional DNA that arises as a vestige of evolutionary history. Because of this view, life scientists and the biomedical research community eschew studying regions of the human genome they deem to be junk DNA. This posture is not unreasonable. It doesn’t make sense to invest precious scientific resources to study nonfunctional DNA.

    Many life scientists are unaware of their bias. Unfortunately, this stereotyping hinders scientific advance by delaying discoveries that could be translated into the clinical setting. Quite often, supposed junk DNA has turned out to serve a vital purpose. Failure to recognize this function not only compromises our understanding of genome biology, but also hinders biomedical researchers from identifying defects in these genomic regions that contribute to genetic diseases and disorders.

    As psychologists will point out, acknowledging bias is the first step to solving the problems that stereotyping causes. This is precisely what these researchers have done by publishing an article in Nature Review Genetics.3 The team focused on DNA sequence elements called pseudogenes. Traditionally, life scientists have viewed pseudogenes as the remnants of once functional genes. Biologists have identified three categories of pseudogenes: (1) unitary, (2) duplicated, and (3) processed.

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    Figure 1: Mechanisms for Formation of Duplicated and Processed Pseudogenes. Image credit: Wikipedia

    Researchers categorize DNA sequences as pseudogenes based on structural features. Such features indicate to the investigators that these sequence elements were functional genes at one time in evolutionary history, but eventually lost function due to mutations or other biochemical processes, such as reverse transcription and DNA insertion. Once a DNA sequence is labeled a pseudogene, bias sets in and researchers just assume that it lacks function—not because it has been experimentally demonstrated to be nonfunctional, but because of the stereotyping that arises out of the evolutionary paradigm.

    The authors of the piece acknowledge that “the annotation of genomics regions as pseudogenes constitutes an etymological signifier that an element has no function and is not a gene. As a result, pseudogene-annotated regions are largely excluded from functional screen and genomic analyses.”4 In other words, the “pseudogene” moniker biases researchers to such a degree that they ignore these sequence elements as they study genome structure and function without ever doing the hard, experimental work to determine whether it is actually nonfunctional.

    This approach is clearly misguided and detracts from scientific discovery. As the authors admit, “However, with a growing number of instances of pseudogene-annotated regions later found to exhibit biological function, there is an emerging risk that these regions of the genome are prematurely dismissed as pseudogenic and therefore regarded as void of function.”5

    Discovering Function Despite Bias

    The harmful effects of this bias become evident as biomedical researchers unexpectedly stumble upon function for pseudogenes, time and time, again, not because of the evolutionary paradigm, but despite it. These authors point out that many processed pseudogenes are transcribed and, of those, many are translated to produce proteins. Many unitary and duplicated pseudogenes are also transcribed. Some are also translated into proteins, but a majority are not. Instead they play a role in gene regulation as described by the competitive endogenous RNA hypothesis.

    Still, there are some pseudogenes that aren’t transcribed and, thus, could rightly be deemed nonfunctional. However, the researchers point out that the current experimental approaches for identifying transcribed regions are less than ideal. Many of these methods may fail to detect pseudogene transcripts. However, as the researchers point out, even if a pseudogene isn’t transcribed it still may serve a functional role (e.g., contributing to chromosome three-dimensional structure and stability).

    This Nature article raises a number of questions and concerns for me as a biochemist:

    • How widespread is this bias?
    • If this type of stereotyping exists toward pseudogenes, does it exist for other classes of junk DNA?
    • How well do we really understand genome structure and function?
    • Do we have the wrong perspective on the genome, one that stultifies scientific advance?
    • Does this bias delay the understanding and alleviation of human health concerns?

    Is the Evolutionary Paradigm the Wrong Framework to Study Genomes?

    Based on this article, I think it is safe to conclude that we really don’t understand the molecular biology of genomes. We are living in the midst of a scientific revolution that is radically changing our view of genome structure and function. The architecture and operations of genomes appear to be far more elegant and sophisticated than anyone ever imagined—at least within the confines of the evolutionary paradigm.

    This insight also leads me to question if the evolutionary paradigm is the proper framework for thinking about genome structure and function. From my perspective, treating biological systems as the Creator’s handiwork provides a superior approach to understanding the genome. A creation model approach promotes scientific advance, particularly when the rationale for the structure and function of a particular biological system is not apparent. This expectation forces researchers to keep an open mind and drives further study of seemingly nonfunctional, purposeless systems with the full anticipation that their functional roles will eventually be uncovered.

    Over the last several years, I have raised concerns about the bias life scientists have harbored as they have worked to characterize the human genome (and genomes of other organisms). It is gratifying to me to see that there are life scientists who, though committed to the evolutionary paradigm, are beginning to recognize this bias as well.

    The first step to addressing the problem of stereotyping—in any sector of society—is to acknowledge that it exists. Often, this step is the hardest one to take. The next step is to put in place structures to help overcome its harmful influence. Could it be that part of the solution to this instance of scientific stereotyping is to grant a creation model approach access to the scientific table?

    Resources

    Pseudogene Function

    The Evolutionary Paradigm Hinders Scientific Advance

    Endnotes
    1. For example, see Joshua Aronson et al., “Unhealthy Interactions: The Role of Stereotype Threat in Health Disparities,” American Journal of Public Health 103 (January 1, 2013): 50–56, doi:10.2105/AJPH.2012.300828.
    2. Seth W. Cheetham, Geoffrey J. Faulkner, and Marcel E. Dinger, “Overcoming Challenges and Dogmas to Understand the Functions of Pseudogenes,” Nature Reviews Genetics 21 (March 2020): 191–201, doi:10.1038/s41576-019-0196-1.
    3. Cheetham, Faulkner, and Dinger, 191–201.
    4. Cheetham, Faulkner, and Dinger, 191–201.
    5. Cheetham, Faulkner, and Dinger, 191–201.
  • New Genetic Evidence Affirms Human Uniqueness

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Mar 04, 2020

    It’s a remarkable discovery—and a bit gruesome, too.

    It is worth learning a bit about some of its unseemly details because this find may have far-reaching implications that shed light on our origins as a species.

    In 2018, a group of locals discovered the remains of a two-year-old male puppy in the frozen mud (permafrost) in the eastern part of Siberia. The remains date to 18,000 years in age. Remarkably, the skeleton, teeth, head, fur, lashes, and whiskers of the specimen are still intact.

    Of Dogs and People

    The Russian scientists studying this find (affectionately dubbed Dogor) are excited by the discovery. They think Dogor can shed light on the domestication of wolves into dogs. Biologists believe that this transition occurred around 15,000 years ago. Is Dogor a wolf? A dog? Or a transitional form? To answer these questions, the researchers have isolated DNA from one of Dogor’s ribs, which they think will provide them with genetic clues about Dogor’s identity—and clues concerning the domestication process.

    Biologists study the domestication of animals because this process played a role in helping to establish human civilization. But biologists are also interested in animal domestication for another reason. They think this insight will tell us something about our identity as human beings.

    In fact, in a separate study, a team of researchers from the University of Milan in Italy used insights about the genetic changes associated with the domestication of dogs, cats, sheep, and cattle to identify genetic features that make human beings (modern humans) stand apart from Neanderthals and Denisovans.1 They conclude that modern humans share some of the same genetic characteristics as domesticated animals, accounting for our unique and distinct facial features (compared to other hominins). They also conclude that our high level of cooperativeness and lack of aggression can be explained by these same genetic factors.

    This work in comparative genomics demonstrates that significant anatomical and behavioral differences exist between humans and hominins, supporting the concept of human exceptionalism. Though the University of Milan researchers carried out their work from an evolutionary perspective, I believe their insights can be recast as scientific evidence for the biblical conception of human nature; namely, creatures uniquely made in God’s image.

    Biological Changes that Led to Animal Domestication

    Biologists believe that during the domestication process, many of the same biological changes took place in dogs, cats, sheep, and cattle. For example, they think that during domestication, mild deficits in neural crest cells resulted. In other words, once animals are domesticated, they produce fewer, less active neural crest cells. These stem cells play a role in neural development; thus, neural crest cell defects tend to make animals friendlier and less aggressive. This deficit also impacts physical features, yielding smaller skulls and teeth, floppy ears, and shorter, curlier tails.

    Life scientists studying the domestication process have identified several genes of interest. One of these is BAZ1B. This gene plays a role in the maintenance of neural crest cells and controls their migration during embryological development. Presumably, changes in the expression of BAZ1B played a role in the domestication process.

    Neural Crest Deficits and Williams Syndrome

    As it turns out, there are two genetic disorders in modern humans that involve neural crest cells: Williams-Beuren syndrome (also called Williams syndrome) and Williams-Beuren region duplication syndrome. These genetic disorders involve the deletion or duplication, respectively, of a region of chromosome 7 (7q11.23). This chromosomal region harbors 28 genes. Craniofacial defects and altered cognitive and behavioral traits characterize these disorders. Specifically, people with these syndromes have cognitive limitations, smaller skulls, and elf-like faces, and they display excessive friendliness.

    Among the 28 genes impacted by the two disorders is the human version of BAZ1B. This gene codes for a type of protein called a transcription factor. (Transcription factors play a role in regulating gene expression.)

    The Role of BAZ1B in Neural Crest Cell Biology

    To gain insight into the role BAZ1B plays in neural crest cell biology, the European research team developed induced pluripotent stem cell lines from (1) four patients with Williams syndrome, (2) three patients with Williams-Beuren region duplication syndrome, and (3) four people without either disorder. Then, they coaxed these cells in the laboratory to develop into neural crest cells.

    Using a technique called RNA interference, they down-regulated BAZ1B in all three types of neural crest cells. By doing this, the researchers learned that changes in the expression of this gene altered the migration rates of the neural crest cells. Specifically, they discovered that neural crest cells developed from patients with Williams-Beuren region duplication syndrome migrated more slowly than control cells (generated from test subjects without either syndrome) and neural crest cells derived from patients with Williams syndrome migrated more rapidly than control cells.

    The discovery that the BAZ1B gene influences neural crest cell migration is significant because these cells have to migrate to precise locations in the developing embryo to give rise to distinct cell types and tissues, including those that form craniofacial features.

    Because BAZ1B encodes for a transcription factor, when its expression is altered, it alters the expression of genes under its control. The team discovered that 448 genes were impacted by down-regulating BAZ1B. They learned that many of these impacted genes play a role in craniofacial development. By querying databases of genes that correlate with genetic disorders, researchers also learned that, when defective, some of the impacted genes are known to cause disorders that involve altered facial development and intellectual disabilities.

    Lastly, the researchers determined that the BAZ1B protein (again, a transcription factor) targets genes that influence dendrite and axon development (which are structures found in neurons that play a role in transmissions between nerve cells).

    BAZ1B Gene Expression in Modern and Archaic Humans

    With these findings in place, the researchers wondered if differences in BAZ1B gene expression could account for anatomical and cognitive differences between modern humans and archaic humans—hominins such as Neanderthals and Denisovans. To carry out this query, the researchers compared the genomes of modern humans to Neanderthals and Denisovans, paying close attention to DNA sequence differences in genes under the influence of BAZ1B.

    This comparison uncovered differences in the regulatory region of genes targeted by the BAZ1B transcription factor, including genes that control neural crest cell activities and craniofacial anatomy. In other words, the researchers discovered significant genetic differences in gene expression among modern humans and Neanderthals and Denisovans. And these differences strongly suggest that anatomical and cognitive differences existed between modern humans and Neanderthals and Denisovans.

    Did Humans Domesticate Themselves?

    The researchers interpret their findings as evidence for the self-domestication hypothesis—the idea that we domesticated ourselves after the evolutionary lineage that led to modern humans split from the Neanderthal/Denisovan line (around 600,000 years ago). In other words, just as modern humans domesticated dogs, cats, cattle, and sheep, we domesticated ourselves, leading to changes in our anatomical features that parallel changes (such as friendlier faces) in the features of animals we domesticated. Along with these anatomical changes, our self-domestication led to the high levels of cooperativeness characteristic of modern humans.

    On one hand, this is an interesting account that does seem to have some experimental support. But on the other, it is hard to escape the feeling that the idea of self-domestication as the explanation for the origin of modern humans is little more than an evolutionary just-so story.

    It is worth noting that some evolutionary biologists find this account unconvincing. One is William Tecumseh Fitch III—an evolutionary biologist at the University of Vienna. He is skeptical of the precise parallels between animal domestication and human self-domestication. He states, “These are processes with both similarities and differences. I also don’t think that mutations in one or a few genes will ever make a good model for the many, many genes involved in domestication.”2

    Adding to this skepticism is the fact that nobody has anything beyond a speculative explanation for why humans would domesticate themselves in the first place.

    Genetic Differences Support the Idea of Human Exceptionalism

    Regardless of the mechanism that produced the genetic differences between modern and archaic humans, this work can be enlisted in support of human uniqueness and exceptionalism.

    Though the claim of human exceptionalism is controversial, a minority of scientists operating within the scientific mainstream embrace the idea that modern humans stand apart from all other extant and extinct creatures, including Neanderthals and Denisovans. These anthropologists argue that the following suite of capacities uniquely possessed by modern humans accounts for our exceptional nature:

    • symbolism
    • open-ended generative capacity
    • theory of mind
    • capacity to form complex social systems

    As human beings, we effortlessly represent the world with discrete symbols. We denote abstract concepts with symbols. And our ability to represent the world symbolically has interesting consequences when coupled with our abilities to combine and recombine those symbols in a countless number of ways to create alternate possibilities. Our capacity for symbolism manifests in the form of language, art, music, and even body ornamentation. And we desire to communicate the scenarios we construct in our minds with other human beings.

    But there is more to our interactions with other human beings than a desire to communicate. We want to link our minds together. And we can do this because we possess a theory of mind. In other words, we recognize that other people have minds just like ours, allowing us to understand what others are thinking and feeling. We also have the brain capacity to organize people we meet and know into hierarchical categories, allowing us to form and engage in complex social networks. Forming these relationships requires friendliness and cooperativeness.

    In effect, these qualities could be viewed as scientific descriptors of the image of God, if one adopts a resemblance view for the image of God.

    This study demonstrates that, at a genetic level, modern humans appear to be uniquely designed to be friendlier, more cooperative, and less aggressive than other hominins—in part accounting for our capacity to form complex hierarchical social structures.

    To put it differently, the unique capability of modern humans to form complex, social hierarchies no longer needs to be inferred from the fossil and archaeological records. It has been robustly established by comparative genomics in combination with laboratory studies.

    A Creation Model Perspective on Human Origins

    This study not only supports human exceptionalism but also affirms RTB’s human origins model.

    RTB’s biblical creation model identifies hominins such as Neanderthals and the Denisovans as animals created by God. These extraordinary creatures possessed enough intelligence to assemble crude tools and even adopt some level of “culture.” However, the RTB model maintains that these hominids were not spiritual creatures. They were not made in God’s image. RTB’s model reserves this status exclusively for Adam and Eve and their descendants (modern humans).

    Our model predicts many biological similarities will be found between the hominins and modern humans, but so too will significant differences. The greatest distinction will be observed in cognitive capacity, behavioral patterns, technological development, and culture—especially artistic and religious expression.

    The results of this study fulfill these two predictions. Or, to put it another way, the RTB model’s interpretation of the hominins and their relationship to modern humans aligns with “mainstream” science.

    But what about the similarities between the genetic fingerprint of modern humans and the genetic changes responsible for animal domestication that involve BAZ1B and genes under its influence?

    Instead of viewing these features as traits that emerged through parallel and independent evolutionary histories, the RTB human origins model regards the shared traits as reflecting shared designs. In this case, through the process of domestication, modern humans stumbled upon the means (breeding through artificial selection) to effect genetic changes in wild animals that resemble some of the designed features of our genome that contribute to our unique and exceptional capacity for cooperation and friendliness.

    It is true: studying the domestication process does, indeed, tell us something exceptionally important about who we are.

    Resources

    Endnotes
    1. Matteo Zanella et al., “Dosage Analysis of the 7q11.23 Williams Region Identifies BAZ1B as a Major Human Gene Patterning the Modern Human Face and Underlying Self-Domestication,” Science Advances 5, no. 12 (December 4, 2019): eaaw7908, doi:10.1126/sciadv.aaw7908.
    2. Michael Price, “Early Humans Domesticated Themselves, New Genetic Evidence Suggests,” Science (December 4, 2019), doi:10.1126/science.aba4534.
  • Ancient DNA Indicates Modern Humans Are One-of-a-Kind

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Feb 19, 2020

    The wonderful thing about tiggers
    Is tiggers are wonderful things!
    Their tops are made out of rubber
    Their bottoms are made out of springs!
    They’re bouncy, trouncy, flouncy, pouncy
    Fun, fun, fun, fun, fun!
    But the most wonderful thing about tiggers is
    I’m the only one!1

    With eight grandchildren and counting (number nine will be born toward the end of February), I have become reacquainted with children’s stories. Some of the stories my grandchildren want to hear are new, but many of them are classics. It is fun to see my grandchildren experiencing the same stories and characters I enjoyed as a little kid.

    Perhaps my favorite children’s book of all time is A. A. Milne’s (1882–1956) Winnie-the-Pooh. And of all the characters that populated Pooh Corner, my favorite character is the ineffable Tigger—the self-declared one-of-a-kind.

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    A. A. Milne. Credit: Wikipedia

    For many people (such as me), human beings are like Tigger. We are one-of-a-kind among creation. As a Christian, I take the view that we are unique and exceptional because we alone have been created in God’s image.

    For many others, the Christian perspective on human nature is unpopular and offensive. Who are we to claim some type of special status? They insist that humans aren’t truly unique and exceptional. We are not fundamentally different from other creatures. If anything, we differ only in degree, not kind. Naturalists and others assert that there is no evidence that human beings bear God’s image. In fact, some would go so far as to claim that creatures such as Neanderthals were quite a bit like us. They maintain that these hominins were “exceptional,” just like us. Accordingly, if we are one-of-a-kind it is because, like Tigger, we have arrogantly declared ourselves to be so, when in reality we are no different from any of the other characters who make their home at Pooh Corner.

    Despite this pervasive and popular challenge to human exceptionalism (and the image-of-God concept), there is mounting evidence that human beings stand apart from all extant creatures (such as the great apes) and extinct creatures (such as Neanderthals). This growing evidence can be marshaled to make a scientific case that as human beings we, indeed, are image bearers.

    As a case in point, many archeological studies affirm human uniqueness and exceptionalism. (See the Resources section for a sampling of some of this work.) These studies indicate that human beings alone possess a suite of characteristics that distinguish us from all other hominins. I regard these qualities as scientific descriptors of the image of God:

    • Capacity for symbolism
    • Ability for open-ended manipulation of symbols
    • Theory of mind
    • Capacity to form complex, hierarchical social structures

    Other studies have identified key differences between the brains of modern humans and Neanderthals. (For a sample of this evidence see the Resources section.) One key difference relates to skull shape. Neanderthals (and other hominins) possessed an elongated skull. In contradistinction, our skull shape is globular. The globularity allows for the expansion of the parietal lobe. This is significant because an expanded parietal lobe explains a number of unique human characteristics:

    • Perception of stimuli
    • Sensorimotor transformation (which plays a role in planning)
    • Visuospatial integration (which provides hand-eye coordination)
    • Imagery
    • Self-awareness
    • Working and long-term memory

    Again, I connect these scientific qualities to the image of God.

    Now, two recent studies add to the case for human exceptionalism. They involve genetic comparisons of modern humans with both Neanderthals and Denisovans. Through the recovery and sequencing of ancient DNA, we have high quality genomes for these hominins that we can analyze and compare to the genomes of modern humans.

    While the DNA sequences of protein-coding genes in modern human genomes and the genomes of these two extant hominins is quite similar, both studies demonstrate that the gene expression is dramatically different. That difference accounts for anatomical differences between humans and these two hominins and suggests that significant cognitive differences exist as well.

    Differences in Gene Regulation

    To characterize gene expression patterns in Neanderthals and Denisovans and compare them to modern humans, researchers from Vanderbilt University (VU) used statistical methods to develop a mathematical model that would predict gene expression profiles from the DNA sequences of genomes.2 They built their model using DNA sequences and gene expression data (measured from RNA produced by transcription) for a set of human genomes. To ensure that their model could be used to assess gene expression for Neanderthals and Denisovans, the researchers paid close attention to the gene expression pattern for genes in the human genome that were introduced when modern humans and Neanderthals presumably interbred and compared their expression to human genes that were not of Neanderthal origin.

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    The Process of Gene Expression. Credit: Shutterstock

    With their model in hand, the researchers analyzed the expression profile for nearly 17,000 genes from the Altai Neanderthal. Their model predicts that 766 genes in the Neanderthal genome had a different expression profile than the corresponding genes in modern humans. As it turns out, the differentially expressed genes in the Neanderthal genomes failed to be incorporated into the human genome after interbreeding took place, suggesting to the researchers that these genes are responsible for key anatomical and physiological differences between modern humans and Neanderthals.

    The VU investigators determined that these 766 differentially expressed genes play roles in reproduction, forming skeletal structures, and the functioning of cardiovascular and immune systems.

    Then, the researchers expanded their analysis to include two other Neanderthal genomes (from the Vindija and Croatian specimens) and the Denisovan genome. The researchers learned that the gene expression profiles of the three Neanderthal genomes were more similar to one another than they were to either the gene expression patterns of modern human and Denisovan genomes.

    This study clearly demonstrates that significant differences existed in the regulation of gene expression in modern humans, Neanderthals, and Denisovans and that these differences account for biological distinctives between the three hominin species.

    Differences in DNA Methylation

    In another study, researchers from Israel compared gene expression profiles in modern human genomes with those from and Neanderthals and Denisovans using a different technique. This method assesses DNA methylation.3 (Methylation of DNA downregulates gene expression, turning genes off.)

    Methylation of DNA influences the degradation process for this biomolecule. Because of this influence, researchers can determine the DNA methylation pattern in ancient DNA by characterizing the damage to the DNA fragments isolated from fossil remains.

    Using this technique, the researchers measured the methylation pattern for genomes of two Neanderthals (Altai and Vindija) and a Denisovan and compared these patterns with genomes recovered from the remains of three modern humans, dating to 45,000 years in age, 8,000 years in age, and 7,000 years in age, respectively. They discovered 588 genes in modern human genomes with a unique DNA methylation pattern, indicating that these genes are expressed differently in modern humans than in Neanderthals and Denisovans. Among the 588 genes, researchers discovered some that influence the structure of the pelvis, facial morphology, and the larynx.

    The researchers think that differences in gene expression may explain the anatomical differences between modern humans and Neanderthals. They also think that this result indicates that Neanderthals lacked the capacity for speech.

    What Is the Relationship between Modern Humans and Neanderthals?

    These two genetic studies add to the extensive body of evidence from the fossil record, which indicates that Neanderthals are biologically distinct from modern humans. For a variety of reasons, some Christian apologists and Intelligent Design proponents classify Neanderthals and modern humans into a single group, arguing that the two are equivalent. But these two studies comparing gene regulation profiles make it difficult to maintain that perspective.

    Modern Humans, Neanderthals, and the RTB Human Origins Model

    RTB’s human origins model regards Neanderthals (and other hominins) as creatures made by God, without any evolutionary connection to modern humans. These extraordinary creatures walked erect and possessed some level of intelligence, which allowed them to cobble together tools and even adopt some level of “culture.” However, our model maintains that the hominins were not spiritual beings made in God’s image. RTB’s model reserves this status exclusively for modern humans.

    Based on our view, we predict that biological similarities will exist among the hominins and modern humans to varying degrees. In this regard, we consider the biological similarities to reflect shared designs, not a shared evolutionary ancestry. We also expect biological differences because, according to our model, the hominins would belong to different biological groups from modern humans.

    We also predict that significant cognitive differences would exist between modern humans and the other hominins. These differences would be reflected in brain anatomy and behavior (inferred from the archeological record). According to our model, these differences reflect the absence of God’s image in the hominins.

    The results of these two studies affirm both sets of predictions that flow from the RTB human origins model. The differences in gene regulation between modern human and Neanderthals is precisely what our model predicts. These differences seem to account for the observed anatomical differences between Neanderthals and modern humans observed from fossil remains.

    The difference in the regulation of genes affecting the larynx is also significant for our model and the idea of human exceptionalism. One of the controversies surrounding Neanderthals relates to their capacity for speech and language. Yet, it is difficult to ascertain from fossil remains if Neanderthals had the anatomical structures needed for the vocalization range required for speech. The differences in the expression profiles for genes that control the development and structure of the larynx in modern humans and Neanderthals suggests that Neanderthals lacked the capacity for speech. This result dovetails nicely with the differences in modern human and Neanderthal brain structure, which suggest that Neanderthals also lacked the neural capacity for language and speech. And, of course, it is significant that there is no conclusive evidence for Neanderthal symbolism in the archeological record.

    With these two innovative genetic studies, the scientific support for human exceptionalism continues to mount. And the wonderful thing about this insight is that it supports the notion that as human beings we are the only ones who bear God’s image and can form a relationship with our Creator.

    Resources

    Behavioral Differences between Humans and Neanderthals

    Biological Differences between Humans and Neanderthals

    Endnotes
    1. Richard M. Sherman and Robert B. Sherman, composers, “The Wonderful Thing about Tiggers” (song), released December 1968.
    2. Laura L. Colbran et al., “Inferred Divergent Gene Regulation in Archaic Hominins Reveals Potential Phenotypic Differences,” Nature Evolution and Ecology 3 (November 2019): 1598-606, doi:10.1038/s41559-019-0996-x.
    3. David Gokhman et al., “Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan,” Science 344, no. 6183 (May 2, 2014): 523–27, doi:1126/science.1250368; David Gokhman et al., “Extensive Regulatory Changes in Genes Affecting Vocal and Facial Anatomy Separate Modern from Archaic Humans,” bioRxiv, preprint (October 2017), doi:10.1101/106955.
  • Cave Art Tells the Story of Human Exceptionalism

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Feb 05, 2020

    Comic books intrigue me. They are a powerful storytelling vehicle. The combination of snapshot-style imagery, along with narration and dialogue, allows the writer and artist to depict action and emotion in a way that isn’t possible using the written word alone. Comic books make it easy to depict imaginary worlds. And unlike film, comics engage the reader in a deeper, more personal way. The snapshot format requires the reader to make use of their imagination to fill in the missing details. In this sense, the reader becomes an active participant in the storytelling process.

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    Figure 1: Speech Bubbles on a Comic Strip Background. Credit: Shutterstock

    In America, comics burst onto the scene in the 1930s, but the oldest comics (at least in Europe) trace their genesis to Rodolphe Töpffer (1799-1846). Considered by many to be “the father of comics,” Töpffer was a Swiss teacher, artist, and author who became well-known for his illustrated books—works that bore similarity to modern-day comics.

     

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    Figure 2: Rodolphe Töpffer, Self Portrait, 1840. Credit: Wikipedia

    Despite his renown, Töpffer wasn’t the first comic book writer and artist. That claim to fame belongs to long forgotten artists from prehistory. In fact, recent work by Australian and Indonesian researchers indicates that comics as a storytelling device dates to earlier than 44,000 years ago.

    Seriously!

    These investigators discovered and characterized cave art from a site on the Indonesian island of Sulawesi that depicts a pig and buffalo hunt. Researchers interpret this mural to be the oldest known recorded story1 —a comic book story on a cave wall.

    This find, and others like it, provide important insight into our origins as human beings. From my perspective as a Christian apologist, this discovery is important for another reason. I see it as affirming the biblical teaching about humanity: God made human beings in his image.

    The Find

    Leading up to this discovery, archeologists had already identified and dated art on cave walls in Sulawesi and Borneo. This art, which includes hand stencils and depictions of animals, dates to older than 40,000 years in age and is highly reminiscent of the cave art of comparable age found in Europe.

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    Figure 3: Hand Stencils from a Cave in Southern Sulawesi. Credit: Wikipedia.

    In December 2017, an archeologist from Indonesia discovered the hunting mural in a cave (now called Leang Bulu’ Sipong 4) in the southern part of Sulawesi. The panel presents the viewer with an ensemble of pigs and small buffalo (called anoas), endemic to Sulawesi. Most intriguing about the artwork is the depiction of smaller human-like figures with animal features such as tails and snouts. In some instances, the figures appear to be holding spears and ropes. Scholars refer to these human-animal depictions as therianthropes.

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    Figure 4: Illustration of a Pig Deer Found in a Cave in Southern Sulawesi. Credit: Wikipedia.

    Dating the Find

    Dating cave art can be notoriously difficult. One approach is to directly date the charcoal pigments used to make the art using radiocarbon methods. Unfortunately, the dates measured by this technique can be suspect because the charcoal used to make the art can be substantially older than the artwork itself.

    Recently, archeologists have developed a new approach to date cave art. This method measures the levels of uranium and thorium in calcite deposits that form on top of the artwork. Calcite is continuously deposited on cave walls due to hydrological activity in the cave. As water runs down the cave walls, calcium carbonate precipitates onto the cave wall surface. Trace amounts of radioactive uranium are included in the calcium carbonate precipitates. This uranium decays into thorium, hence the ratio of uranium to thorium provides a measure of the calcite deposit’s age and, in turn, yields a minimum age for the artwork.

    To be clear, this dating method has been the subject of much controversy. Some archeologists argue that the technique is unreliable because the calcite deposits are an open system. Once the calcite deposit forms, water will continue to flow over the surface. The water will solubilize part of the calcite deposit and along with it the trace amounts of uranium and thorium. Thus, because uranium is more soluble than thorium we get an artificially high level of thorium. So, when the uranium-thorium ratio is measured, it may make it appear as if the cave art is older than it actually is.

    To ensure that the method worked as intended, the researchers only dated calcite deposits that weren’t porous (which is a sign that they have been partially re-dissolved) and they made multiple measurements from the surface of the deposit toward the interior. If this sequence of measurements produced a chronologically consistent set of ages, the researchers felt comfortable with the integrity of the calcite samples. Using this method, the researchers determined that the cave painting of the pig and buffalo hunt dates to older than 43,900 years.

    Corroborating evidence gives the archeologists added confidence in this result. For example, the discovery of archeological finds in the Sulawesi cave site that were independently dated indicate that modern humans were in the caves between 40,000 to 50,000 years ago, in agreement with the measured age of the cave art.

    The research team also noted that the animal and the therianthropes in the mural appear to have been created at the same time. This insight is important because therianthropes don’t appear in the cave paintings found in Europe until around 10,000 years ago. This observation means that it is possible that the therianthropes could have been added to the painting millennia after the animals were painted onto the cave wall. However, the researchers don’t think this is the case for at least three reasons. First, the same artistic style was used to depict the animals and therianthropes. Second, the technique and pigment used to create the figures is the same. And third, the degree of weathering is the same throughout the panel. None of these features would be expected if the therianthropes were a late addition to the mural.

    Interpreting the Find

    The researchers find the presence of therianthropes in 44,000+ year-old cave art significant. It indicates that humans in Sulawesi not only possessed the capacity for symbolism, but, more importantly, had the ability to conceive of things that did not exist in the material world. That is to say, they had a sense of the supernatural.

    Some archeologists believe that the cave art reflects shamanic beliefs and visions. If this is the case, then it suggests that the therianthropes in the painting may reflect spirit animal helpers who ensured the success of the hunt. The size of the therianthropes supports this interpretation. These animal-human hybrids are depicted as much smaller than the pigs and buffalo. On the island of Sulawesi, both the pig and buffalo species in question were much smaller than modern humans.

    Because this artwork depicts a hunt involving therianthropes, the researchers see rich narrative content in the display. It seems to tell a story that likely reflected the mythology of the Sulawesi people. You could say it’s a comic book on a cave wall.

    Relationship between Cave Art in Europe and Asia

    Cave art in Europe has been well-known and carefully investigated by archeologists and anthropologists for nearly a century. Now archeologists have access to a growing archeological record in Asia.

    Art found at these sites is of the same quality and character as the European cave art. However, it is older. This discovery means that modern humans most likely had the capacity to make art even before beginning their migrations around the world from out of Africa (around 60,000 years ago).

    As noted, the discovery of therianthropes at 44,000+ years in age in Sulawesi is intriguing because these types of figures don’t appear in cave art in Europe until around 10,000 years ago. But archeologists have discovered the lion-man statue in a cave site in Germany. This artifact, which depicts a lion-human hybrid, dates to around 40,000 years in age. In other words, therianthropes were part of the artwork of the first Europeans. It also indicates that modern humans in Europe had the capacity to envision imaginary worlds and held belief in a supernatural realm.

    Capacity for Art and the Image of God

    For many people, our ability to create and contemplate art serves as a defining feature of humanity—a quality that reflects our capacity for sophisticated cognitive processes. So, too, does our capacity for storytelling. As humans, we seem to be obsessed with both. Art and telling stories are manifestations of symbolism and open-ended generative capacity. Through art (as well as music and language), we express and communicate complex ideas and emotions. We accomplish this feat by representing the world—and even ideas—with symbols. And, we can manipulate symbols, embedding them within one another to create alternate possibilities.

    As a Christian, I believe that our capacity to make art and to tell stories is an outworking of the image of God. As such, the appearance of art (as well as other artifacts that reflect our capacity for symbolism) serves as a diagnostic for the image of God in the archeological record. That record provides the means to characterize the mode and tempo of the appearance of behavior that reflect the image of God. If the biblical account of human origins is true, then I would expect that artistic expression should be unique to modern humans and should appear at the same time that we make our first appearance as a species.

    So, when did art (and symbolic capacity) first appear? Did art emerge suddenly? Did it appear gradually? Is artistic expression unique to human beings or did other hominins, such as Neanderthals, produce art too? Answers to these questions are vital to our case for human exceptionalism and, along with it, the image of God.

    When Did the Capacity for Art First Appear?

    Again, the simultaneous appearance of cave art in Europe and Asia indicates that the capacity for artistic expression (and, hence, symbolism) dates back to the time in prehistory before humans began to migrate around the world from out of Africa (around 60,000 years ago). This conclusion gains support from the recent discovery of a silcrete flake from a layer in the Blombos Cave that dates to about 73,000 years old. (The Blombos Cave is located around 150 miles east of Cape Town, South Africa.) A portion of an abstract drawing is etched into this flake.2

    Linguist Shigeru Miyagawa believes that artistic expression emerged in Africa earlier than 125,000 years ago. Archeologists have discovered rock art produced by the San people that dates to 72,000 years ago. This art shares certain elements with European cave art. Because the San diverged from the modern human lineage around 125,000 years ago, the ancestral people groups that gave rise to both lines must have possessed the capacity for artistic expression before that time.3

    It is also significant that the globular brain shape of modern humans first appears in the archeological record around 130,000 years ago. As I have written about previously, globular brain shape allows expansion of the parietal lobe, which is responsible for many of our capacities:

    • Perception of stimuli
    • Sensorimotor transformation (which plays a role in planning)
    • Visuospatial integration (which provides hand-eye coordination needed for making art)
    • Imagery
    • Self-awareness
    • Working and long-term memory

    In other words, the evidence indicates that our capacity for symbolism emerged at the time that our species first appears in the fossil record. Some archeologists claim that Neanderthals displayed the capacity for symbolism as well. If this claim proves true, then human beings don’t stand apart from other creatures. We aren’t special.

    Did Neanderthals Have the Capacity to Create Art?

    Claims of Neanderthal artistic expression abound in popular literature and appear in scientific journals. However, a number of studies question these claims. When taken as a whole, the evidence indicates that Neanderthals were cognitively inferior to modern humans.

    So, when the evidence is considered as a whole, only human beings (modern humans) possess the capability for symbolism, open-ended generative capacity, and theory of mind—in my view, scientific descriptors of the image of God. The archeological record affirms the biblical view of human nature. It is also worth noting that the origin of our symbolic capacity seems to arise at the same time that modern humans appear in the fossil record, an observation I would expect given the biblical account of human origins.

    Like the comics that intrigue me, this narrative resonates on a personal level. It seems as if the story told in the opening pages of the Old Testament is true.

    Resources

    Cave Art and the Image of God

    The Modern Human Brain

    Could Neanderthals Make Art?

    Endnotes
    1. Maxime Aubert et al., “Earliest Hunting Scene in Prehistoric Art,” Nature 576 (December 11, 2019): 442–45, doi:10.1038/s41586-019-1806y.
    2. Shigeru Miyagawa, Cora Lesure, and Vitor A. Nóbrega, “Cross-Modality Information Transfer: A Hypothesis about the Relationship among Prehistoric Cave Paintings, Symbolic Thinking, and the Emergence of Language,” Frontiers in Psychology 9 (February 20, 2018): 115, doi:10.3389/fpsyg.2018.00115.
    3. Christopher S. Henshilwood et al., “An Abstract Drawing from the 73,000-Year-Old Levels at Blombos Cave, South Africa,” Nature 562 (September 12, 2018): 115–18, doi:10.1038/s41586-018-0514-3.
  • But Do Watches Replicate? Addressing a Logical Challenge to the Watchmaker Argument

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jan 22, 2020

    Were things better in the past than they are today? It depends who you ask.

    Without question, there are some things that were better in years gone by. And, clearly, there are some historical attitudes and customs that, today, we find hard to believe our ancestors considered to be an acceptable part of daily life.

    It isn’t just attitudes and customs that change over time. Ideas change, too—some for the better, some for the worst. Consider the way doing science has evolved, particularly the study of biological systems. Was the way we approached the study of biological systems better in the past than it is today?

    It depends who you ask.

    As an old-earth creationist and intelligent design proponent, I think the approach biologists took in the past was better than today for one simple reason. Prior to Darwin, teleology was central to biology. In the late 1700s and early to mid-1800s, life scientists viewed biological systems as the product of a Mind. Consequently, design was front and center in biology.

    As part of the Darwinian revolution, teleology was cast aside. Mechanism replaced agency and design was no longer part of the construct of biology. Instead of reflecting the purposeful design of a Mind, biological systems were now viewed as the outworking of unguided evolutionary mechanisms. For many people in today’s scientific community, biology is better for it.

    Prior to Darwin, the ideas shaped by thinkers (such as William Paley) and biologists (such as Sir Richard Owen) took center stage. Today, their ideas have been abandoned and are often lampooned.

    But, advances in my areas of expertise (biochemistry and origins-of-life research) justify a return to the design hypothesis, indicating that there may well be a role for teleology in biology. In fact, as I argue in my book The Cell’s Design, the latest insights into the structure and function of biomolecules bring us full circle to the ideas of William Paley (1743-1805), revitalizing his Watchmaker argument for God’s existence.

    In my view, many examples of molecular-level biomachinery stand as strict analogs to human-made machinery in terms of architecture, operation, and assembly. The biomachines found in the cell’s interior reveal a diversity of form and function that mirrors the diversity of designs produced by human engineers. The one-to-one relationship between the parts of man-made machines and the molecular components of biomachines is startling (e.g., the flagellum’s hook). I believe Paley’s case continues to gain strength as biochemists continue to discover new examples of biomolecular machines.

    The Skeptics’ Challenge

    Despite the powerful analogy that exists between machines produced by human designers and biomolecular machines, many skeptics continue to challenge the revitalized watchmaker argument on logical grounds by arguing in the same vein as David Hume.1 These skeptics assert that significant and fundamental differences exist between biomachines and human creations.

    In a recent interaction on Twitter, a skeptic raised just such an objection. Here is what he wrote:

    “Do [objects and machines designed by humans] replicate with heritable variation? Bad analogy, category mistake. Same one Paley made with his watch on the heath centuries ago.”

    In other words, biological systems replicate, whereas devices and artefacts made by human beings don’t. This difference is fundamental. Such a dissimilarity is so significant that it undermines the analogy between biological systems (in general) and biomolecular machines (specifically) and human designs, invalidating the conclusion that life must stem from a Mind.

    This is not the first time I have encountered this objection. Still, I don’t find it compelling because it fails to take into account manmade machines that do, indeed, replicate.

    Von Neumann’s Universal Self-Constructor

    In the 1940s, mathematician, physicist, and computer scientist John von Neumann (1903–1957) designed a hypothetical machine called a universal constructor. This machine is a conceptual apparatus that can take materials from the environment and build any machine, including itself. The universal constructor requires instructions to build the desired machines and to build itself. It also requires a supervisory system that can switch back and forth between using the instructions to build other machines and copying the instructions prior to the replication of the universal constructor.

    Von Neumann’s universal constructor is a conceptual apparatus, but today researchers are actively trying to design and build self-replicating machines.2 Much work needs to be done before self-replicating machines are a reality. Nevertheless, one day machines will be able to reproduce, making copies of themselves. To put it another way, reproduction isn’t necessarily a quality that distinguishes machines from biological systems.

    It is interesting to me that a description of von Neumann’s universal constructor bears remarkable similarity to a description of a cell. In fact, in the context of the origin-of-life problem, astrobiologists Paul Davies and Sara Imari Walker noted the analogy between the cell’s information systems and von Neumann’s universal constructor.3 Davies and Walker think that this analogy is key to solving the origin-of-life problem. I would agree. However, Davies and Walker support an evolutionary origin of life, whereas I maintain that the analogy between cells and von Neumann’s universal constructor adds vigor to the revitalized Watchmaker argument and, in turn, the scientific case for a Creator.

    In other words, the reproduction objection to the Watchmaker argument has little going for it. Self-replication is not the basis for viewing biomolecular machines as fundamentally dissimilar to machines created by human designers. Instead, self-replication stands as one more machine-like attribute of biochemical systems. It also highlights the sophistication of biological systems compared to systems produced by human designers. We are a far distance away from creating machines that are as sophisticated as the machines found inside the cell. Nevertheless, as we continue to move in that direction, I think the case for a Creator will become even more compelling.

    Who knows? With insights such as these maybe one day we will return to the good old days of biology, when teleology was paramount.

    Resources

    Biomolecular Machines and the Watchmaker Argument

    Responding to Challenges to the Watchmaker Argument

    Endnotes
    1. Whenever you depart, in the least, from the similarity of the cases, you diminish proportionably the evidence; and may at last bring it to a very weak analogy, which is confessedly liable to error and uncertainty.” David Hume, “Dialogues Concerning Natural Religion,” in Classics of Western Philosophy, 3rd ed., ed. Steven M. Cahn, (1779; repr., Indianapolis: Hackett, 1990), 880.
    2. For example, Daniel Mange et al., “Von Neumann Revisited: A Turing Machine with Self-Repair and Self-Reproduction Properties,” Robotics and Autonomous Systems 22 (1997): 35-58, https://doi.org/10.1016/S0921-8890(97)00015-8; Jean-Yves Perrier, Moshe Sipper, and Jacques Zahnd, “Toward a Viable, Self-Reproducing Universal Computer,” Physica D: Nonlinear Phenomena
      97, no. 4 (October 15, 1996): 335–52, https://doi.org/10.1016/0167-2789(96)00091-7; Umberto Pesavento, “An Implementation of von Neumann’s Self-Reproducing Machine,” Artificial Life 2, no. 4 (Summer 1995): 337–54, https://doi.org/10.1162/artl.1995.2.4.337.
    3. Sara Imari Walker and Paul C. W. Davies, “The Algorithmic Origins of Life,” Journal of the Royal Society Interface 10 (2013), doi:10.1098/rsif.2012.0869.
  • The Flagellum’s Hook Connects to the Case for a Creator

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jan 08, 2020

    What would you say is the most readily recognizable scientific icon? Is it DNA, a telescope, or maybe a test tube?

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    Figure 1: Scientific Icons. Image credit: Shutterstock

    Marketing experts recognize the power of icons. When used well, icons prompt consumers to instantly identify a brand or product. They can also communicate a powerful message with a single glance.

    Though many skeptics question if it’s science at all, the intelligent design movement has identified a powerful icon that communicates its message. Today, when most people see an image the bacterial flagellum they immediately think: Intelligent Design.

    This massive protein complex powerfully communicates sophisticated engineering that could only come from an Intelligent Agent. And along these lines, it serves as a powerful piece of evidence for a Creator’s handiwork. Careful study of its molecular architecture and operation provides detailed evidence that an Intelligent Agent must be responsible for biochemical systems and, hence, the origin of life. And, as it turns out, the more we learn about the bacterial flagellum, the more evident it becomes that a Creator must have played a role in the origin and design of life—at least at the biochemical levelas new research from Japan illustrates.1

    The Bacterial Flagellum

    This massive protein complex looks like a whip extending from the bacterial cell surface. Some bacteria have only a single flagellum, others possess several flagella. Rotation of the flagellum(a) allows the bacterial cell to navigate its environment in response to various chemical signals.

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    Figure 2: Typical Bacteria with Flagella. Image credit: Shutterstock

    An ensemble of 30 to 40 different proteins makes up the typical bacterial flagellum. These proteins function in concert as a literal rotary motor. The flagellum’s components include a rotor, stator, drive shaft, bushing, universal joint, and propeller. It is essentially a molecular-sized electrical motor directly analogous to human-produced rotary motors. The rotation is powered by positively charged hydrogen ions flowing through the motor proteins embedded in the inner membrane.

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    Figure 3: The Bacterial Flagellum. Image credit: Wikipedia

    The Bacterial Flagellum and the Revitalized Watchmaker Argument

    Typically, when intelligent design proponents/creationists use the bacterial flagellum to make the case for a Creator, they focus the argument on its irreducibly complex nature. I prefer a different tact. I like to emphasize the eerie similarity between rotary motors created by human designers and nature’ bacterial flagella.

    The bacterial flagellum is just one of a large number of protein complexes with machine-like attributes. (I devote an entire chapter to biomolecular machines in my book The Cell’s Design.) Collectively, these biomolecular machines can be deployed to revitalize the Watchmaker argument.

    Popularized by William Paley in the eighteenth century, this argument states that as a watch requires a watchmaker, so too, life requires a Creator. Following Paley’s line of reasoning, a machine is emblematic of systems produced by intelligent agents. Biomolecular machines display the same attributes as human-crafted machines. Therefore, if the work of intelligent agents is necessary to explain the genesis of machines, shouldn’t the same be true for biochemical systems?

    Skeptics inspired by atheist philosopher David Hume have challenged this simple, yet powerful, analogy. They argue that the analogy would be compelling only if there is a high degree of similarity between the objects that form the analogy. Skeptics have long argued that biochemical systems and machines are too dissimilar to make the Watchmaker argument work.

    However, the striking similarity between the machine parts of the bacterial flagellum and human-made machines cause this objection to evaporate. New work on flagella by Japanese investigators lends yet more support to the Watchmaker analogy.

    New Insights into the Structure and Function of the Flagellum’s Universal Joint

    The flagellum’s universal joint (sometimes referred to as the hook) transfers the torque generated by the motor to the propeller. The research team wanted to develop a deeper understanding of the relationship between the molecular structure of the hook and how the structural features influence its function as a universal joint.

    Comprised of nearly 100 copies (monomers) of a protein called FlgE, the hook is a curved, tube-like structure with a hollow interior. FlgE monomers stack on top of each other to form a protofilament. Eleven protofilaments organize to form the hook’s tube, with the long axis of the protofilament aligning to form the long axis of the hook.

    Each FlgE monomer consists of three domains, called D0, D1, and D2. The researchers discovered that when the FlgE monomers stack to form a protofilament, the D0, D1, and D2 domains of each of the monomers align along the length of the protofilament to form three distinct regions in the hook. These layers have been labeled the tube layer, the mesh layer, and the spring layer.

    During the rotation of the flagellum, the protofilaments experience compression and extension. The movement of the domains, which changes their spatial arrangement relative to one another, mediates the compression and extension. These domain movements allow the hook to function as a universal joint that maintains a rigid tube shape against a twisting “force,” while concurrently transmitting torque from the motor to the flagellum’s filament as it bends along its axis.

    Regardless of one’s worldview, it is hard not to marvel at the sophisticated and elegant design of the flagellum’s hook!

    The Bacterial Flagellum and the Case for a Creator

    If the Watchmaker argument holds validity, it seems reasonable to think that the more we learn about protein complexes, such as the bacterial flagellum, the more machine-like they should appear to be. This work by the Japanese biochemists bears out this assumption. The more we characterize biomolecular machines, the more reason we have to think that life stems from a Creator’s handiwork.

    Dynamic properties of the hook assembly add to the Watchmaker argument (when applied to the bacterial flagellum). This structure is much more sophisticated and ingenious than the design of a typical universal joint crafted by human designers. This elegance and ingenuity of the hook are exactly the attributes I would expect if a Creator played a role in the origin and design of life.

    Message received, loud and clear.

    Resources

    The Bacterial Flagellum and the Case for a Creator

    Can Intelligent Design Be Part of the Scientific Construct?

    Endnotes
    1. Takayuki Kato et al., “Structure of the Native Supercoiled Flagellar Hook as a Universal Joint,” Nature Communications 10 (2019): 5295, doi:10.1038/s4146.
  • Genome Code Builds the Case for Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Dec 18, 2019

    A few days ago, I was doing a bit of Christmas shopping for my grandkids and I happened across some really cool construction kits, designed to teach children engineering principles while encouraging imaginative play. For those of you who still have a kid or two on your Christmas list, here are some of the products that caught my eye:

    These building block sets are a far cry from the simple Lego kits I played with as a kid.

    As cool as these construction toys may be, they don’t come close to the sophisticated construction kit cells use to build the higher-order structures of chromosomes. This point is powerfully illustrated by the insights of Italian investigator Giorgio Bernardi. Over the course of the last several years, Bernardi’s research teams have uncovered design principles that account for chromosome structure, a set of rules that he refers to as the genome code.1

    To appreciate these principles and their theological implications, a little background information is in order. (For those readers familiar with chromosome structure, skip ahead to The Genome Code.)

    Chromosomes

    DNA and proteins interact to make chromosomes. Each chromosome consists of a single DNA molecule wrapped around a series of globular protein complexes. These complexes repeat to form a supramolecular structure resembling a string of beads. Biochemists refer to the “beads” as nucleosomes.

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    Figure 1: Nucleosome Structure. Image credit: Shutterstock

    The chain of nucleosomes further coils to form a structure called a solenoid. In turn, the solenoid condenses to form higher-order structures that constitute the chromosome.

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    Figure 2: Chromosome Structure Image credit: Shutterstock

    Between cell division events (called the interphase of the cell cycle), the chromosome exists in an extended diffuse form that is not readily detectable when viewed with a microscope. Just prior to and during cell division, the chromosome condenses to form its readily recognizable compact structures.

    Biologists have discovered that there are two distinct regions—labeled euchromatin and heterochromatin for chromosomes in the diffuse state. Euchromatin is resistant to staining with dyes that help researchers view it with a microscope. On the other hand, heterochromatin stains readily. Biologists believe that heterochromatin is more tightly packed (and, hence, more readily stained) than euchromatin. They have also learned that heterochromatin associates with the nuclear envelope.

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    Figure 3: Structure of the Nucleus Showing the Distribution of Euchromatin and Heterochromatin. Image credit: Wikipedia

    The Genome Code

    Historically, biologists have viewed chromosomes as consisting of compositionally distinct units called isochores. In vertebrate genomes, five isochores exist (L1, L2, H1, H2, and H3). The isochores differ in the composition of guanine- and cytosine-containing deoxyribonucleotides (two of the four building blocks of DNA). The GC composition increases from L1 to H3. Gene density also increases, with the H3 isochore possessing the greatest number of genes. On the other hand, the size of DNA pieces of compositional homogeneity decreases from L1 to H3.

    Bernardi and his collaborators have developed evidence that the isochores reflect a fundamental unit of chromosome organization. The H isochores correspond to GC-rich euchromatin (containing most of the genes) and the L isochores correspond to GC-poor heterochromatin (characterized by gene deserts).

    Bernardi’s research teams have demonstrated that the two groups of isochores are characterized by different distributions of DNA sequence elements. GC-poor isochores contain a disproportionately high level of oligo A sequences while GC-rich isochores harbor a disproportionately high level of oligo G sequences. These two different types of DNA sequence elements form stiff structures that mold the overall three-dimensional architecture of chromosomes. For example, oligo A sequences introduce curvature to the DNA double helix. This topology allows the double helix to wrap around the protein core that forms nucleosomes. The oligo G sequence elements adopt a topology that weakens binding to the proteins that form the nucleosome core. As Bernardi points out, “There is a fundamental link between DNA structure and chromatin structure, the genomic code.”2

    In other words, the genomic code refers to a set of DNA sequence elements that:

    1. Directly encodes and molds chromosome structure (while defining nucleosome binding),
    2. Is pervasive throughout the genome, and
    3. Overlaps the genetic code by constraining sequence composition and gene structure.

    Because of the existence of the genomic code, variations in DNA sequence caused by mutations will alter the structure of chromosomes and lead to deleterious effects.

    The bottomline: Most of the genomic sequence plays a role in establishing the higher-order structures necessary for chromosome formation.

    Genomic Code Challenges the Junk DNA Concept

    According to Bernardi, the discovery of the genomic code explains the high levels of noncoding DNA sequences in genomes. Many people view such sequences as vestiges of an evolutionary history. Because of the existence and importance of the genomic code, the vast proportion of noncoding DNA found in vertebrate genomes must be viewed as functionally vital. According to Bernardi:

    Ohno, mostly focusing on pseudo-genes, proposed that non-coding DNA was “junk DNA.” Doolittle and Sapienza and Orgel and Crick suggested the idea of “selfish DNA,” mainly involving transposons visualized as molecular parasites rather than having an adaptive function for their hosts. In contrast, the ENCODE project claimed that the majority (~80%) of the genome participated “in at least one biochemical RNA-and/or chromatin-associated event in at least one cell type.”…At first sight, the pervasive involvement of isochores in the formation of chromatin domains and spatial compartments seems to leave little or no room for “junk” or “selfish” DNA.3

    The ENCODE Project

    Over the last decade or so, ENCODE Project scientists have been seeking to identify the functional DNA sequence elements in the human genome. The most important landmark for the project came in the fall of 2012 when the ENCODE Project reported phase II results. (Currently, ENCODE is in phase IV.) To the surprise of many, the project reported that around 80 percent of the human genome displays biochemical activity—hence, function—with many scientists anticipating that that percentage would increase as phases III and IV moved toward completion.

    The ENCODE results have generated quite a bit of controversy, to say the least. Some researchers accept the ENCODE conclusions. Others vehemently argue that the conclusions fly in the face of the evolutionary paradigm and, therefore, can’t be valid. Of course, if the ENCODE Project conclusions are correct, then it becomes a boon for creationists and intelligent design advocates.

    One of the most prominent complaints about the ENCODE conclusions relates to the way the consortium determined biochemical function. Critics argue that ENCODE scientists conflated biochemical activity with function. These critics assert that, at most, about ten percent of the human genome is truly functional, with the remainder of the activity reflecting biochemical noise and experimental artifacts.

    However, as Bernardi points out, his work (independent of the ENCODE Project) affirms the project’s conclusions. In this case, the so-called junk DNA plays a critical role in molding the structures of chromosomes and must be considered functional.

    Function for “Junk DNA”

    Bernardi’s work is not the first to recognize pervasive function of noncoding DNA. Other researchers have identified other functional attributes of noncoding DNA. To date, researchers have identified at least five distinct functional roles that noncoding DNA plays in genomes.

    1. Helps in gene regulation
    2. Functions as a mutational buffer
    3. Forms a nucleoskeleton
    4. Serves as an attachment site for mitotic apparatus
    5. Dictates three-dimensional architecture of chromosomes

    A New View of Genomes

    These types of insights are forcing us to radically rethink our view of the human genome. It appears that genomes are incredibly complex, sophisticated biochemical systems and most of the genes serve useful and necessary functions.

    We have come a long way from the early days of the human genome project. Just 15 years ago, many scientists estimated that around 95 percent of the human genome consists of junk. That acknowledgment seemingly provided compelling evidence that humans must be the product of an evolutionary history. Today, the evidence suggests that the more we learn about the structure and function of genomes, the more elegant and sophisticated they appear to be. It is quite possible that most of the human genome is functional.

    For creationists and intelligent design proponents, this changing view of the human genome provides reasons to think that it is the handiwork of our Creator. A skeptic might wonder why a Creator would make genomes littered with so much junk. But if a vast proportion of genomes consists of functional sequences, then this challenge no longer carries weight and it becomes more and more reasonable to interpret genomes from within a creation model/intelligent design framework.

    What a Christmas gift!

    Resources

    Junk DNA Regulates Gene Expression

    Junk DNA Serves as a Mutational Buffer

    Junk DNA Serves a Nucleoskeletal Role

    Junk DNA Plays a Role in Cell Division

    ENCODE Project

    Studies that Affirm the ENCODE Results

    Endnotes
    1. Giorgio Bernardi, “The Genomic Code: A Pervasive Encoding/Molding of Chromatin Structures and a Solution of the ‘Non-Coding DNA’ Mystery,” BioEssays 41, no. 12 (November 8, 2019), doi:10.1002/bies.201900106.
    2. Bernardi, “The Genomic Code.
    3. Bernardi, “The Genomic Code.
  • Mutations, Cancer, and the Case for a Creator

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Dec 11, 2019

    Cancer. Perhaps no other word evokes more fear, anger, and hopelessness.

    It goes without saying that cancer is an insidious disease. People who get cancer often die way too early. And even though a cancer diagnosis is no longer an immediate death sentence—thanks to biomedical advances—there are still many forms of cancer that are difficult to manage, let alone effectively treat.

    Cancer also causes quite a bit of consternation for those of us who use insights from science to make a case for a Creator. From my vantage point, one of the most compelling reasons to think that a Creator exists and played a role in the origin and design of life is the elegant, sophisticated, and ingenious designs of biochemical systems. And yet, when I share this evidence with skeptics—and even seekers—I am often met with resistance in the form of the question: What about cancer?

    Why Would God Create a World Where Cancer Is Possible?

    In effect, this question typifies one of the most commonand significantobjections to the design argument. If a Creator is responsible for the designs found in biochemistry, then why are so many biochemical systems seemingly flawed, inelegant, and poorly designed?

    The challenge cancer presents for the design argument carries an added punch. It’s one thing to cite inefficiency of protein synthesis or the error-prone nature of the rubisco enzyme, but it’s quite another to describe the suffering of a loved one who died from cancer. There’s an emotional weight to the objection. These deaths feel horribly unjust.

    Couldn’t a Creator design biochemistry so that a disease as horrific as cancer would never be possible—particularly if this Creator is all-powerful, all-knowing, and all-good?

    I think it’s possible to present a good answer to the challenge that cancer (and other so-called bad designs) poses for the design argument. Recent insights published by a research duo from Cambridge University in the UK help make the case.1

    A Response to the Bad Designs in Biochemistry and Biology

    Because the “bad designs” challenge is so significant (and so frequently expressed), I devoted an entire chapter in The Cell’s Design to addressing the apparent imperfections of biochemical systems. My goal in that chapter was to erect a framework that comprehensively addresses this pervasive problem for the design argument.

    In the face of this challenge it is important to recognize that many so-called biochemical flaws are not genuine flaws at all. Instead, they arise as the consequences of trade-offs. In their cellular roles, many biochemical systems face two (or more) competing objectives. Effectively managing these opposing objectives means that it is impossible for every aspect of the system to perform at an optimal level. Some features must be carefully rendered suboptimal to ensure that the overall system performs robustly under a wide range of conditions.

    Cancer falls into this category. It is not a consequence of flawed biochemical designs. Instead, cancer reflects a trade-off between DNA repair and cell survival.

    DNA Damage and Cancer

    The etiology (cause) of most cancers is complex. While about 10 percent of cancers have a hereditary basis, the vast proportion results from mutations to DNA caused by environmental factors.

    Some of the damage to DNA stems from endogenous (internal) factors, such as water and oxygen in the cell. These materials cause hydrolysis and oxidative damage to DNA, respectively. Both types of damage can introduce mutations into this biomolecule. Exogenous chemicals (genotoxins) from the environment can also interact with DNA and cause damage leading to mutations. So does exposure to ultraviolet radiation and radioactivity from the environment.

    Infectious agents such as viruses can also cause cancer. Again, these infectious agents cause genomic instability, which leads to DNA mutations.

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    Figure: Tumor Formation Process. Image credit: Shutterstock

    In effect, DNA mutations are an inevitable consequence of the laws of nature, specifically the first and second laws of thermodynamics. These laws make possible the chemical structures and operations necessary for life to even exist. But, as a consequence, these same life-giving laws also undergird chemical and physical processes that damage DNA.

    Fortunately, cells have the capacity to detect and repair damage to DNA. These DNA repair pathways are elaborate and sophisticated. They are the type of biochemical features that seem to support the case for a Creator. DNA repair pathways counteract the deleterious effects of DNA mutation by correcting the damage and preventing the onset of cancer.

    Unfortunately, these DNA repair processes function incompletely. They fail to fully compensate for all of the damage that occurs to DNA. Consequently, over time, mutations accrue in DNA, leading to the onset of cancer. The inability of the cell’s machinery to repair all of the mutation-causing DNA damage and, ultimately, protect humans (and other animals) from cancer is precisely the thing that skeptics and seekers alike point to as evidence that counts against intelligent design.

    Why would a Creator make a world where cancer is possible and then design cancer-preventing processes that are only partially effective?

    Cancer: The Result of a Trade-Off

    Even though mutations to DNA cause cancer, it is rare that a single mutation leads to the formation of a malignant cell type and, subsequently, tumor growth. Biomedical researchers have discovered that the onset of cancer involves a series of mutations to highly specific genes (dubbed cancer genes). The mutations that cause cells to transform into cancer cells are referred to as driver mutations. Researchers have also learned that most cells in the body harbor a vast number of mutations that have little or no biological consequence. These mutations are called passenger mutations. As it turns out, there are thousands of passenger mutations in a typical cancer cell and only about ten driver mutations to so-called cancer genes. Biomedical investigators have also learned that many normal cells harbor both passenger and driver mutations without ever transforming. (It appears that other factors unrelated to DNA mutation play a role in causing a cancer cell to undergo extensive clonal expansion, leading to the formation of a tumor.)

    What this means is that mutations to DNA are quite extensive, even in normal, healthy cells. But this factor prompts the question: Why is the DNA repair process so lackluster?

    The research duo from Cambridge University speculate that DNA repair is so costly to cells—making extensive use of energy and cell resources—that to maintain pristine genomes would compromise cell survival. These researchers conclude that “DNA quality control pathways are fully functional but naturally permissive of mutagenesis even in normal cells.”2 And, it seems as if the permissiveness of the DNA repair processes generally have little consequence given that a vast proportion of the human genome consists of noncoding DNA.

    Biomedical researchers have uncovered another interesting feature about the DNA repair processes. The processes are “biased,” with repairs taking place preferentially on the DNA strand (of the double helix) that codes for proteins and, hence, is transcribed. In other words, when DNA repair takes place it occurs where it counts the most. This bias displays an elegant molecular logic and rationale, strengthening the case for design.

    Given that driver mutations are not in and of themselves sufficient to lead to tumor formation, the researchers conclude that cancer prevention pathways are quite impressive in the human body. They conclude, “Considering that an adult human has ~30 trillion cells, and only one cell develops into a cancer, human cells are remarkably robust at preventing cancer.”3

    So, what about cancer?

    Though cancer ravages the lives of so many people, it is not because of poorly designed, substandard biochemical systems. Given that we live in a universe that conforms to the laws of thermodynamics, cancer is inevitable. Despite this inevitability, organisms are designed to effectively ward off cancer.

    Ironically, as we gain a better understanding of the process of oncogenesis (the development of tumors), we are uncovering more—not less—evidence for the remarkably elegant and ingenious designs of biochemical systems.

    The insights by the research team from Cambridge University provide us with a cautionary lesson. We are often quick to declare a biochemical (or biological) feature as poorly designed based on incomplete understanding of the system. Yet, inevitably, as we learn more about the system we discover an exquisite rationale for why things are the way they are. Such knowledge is consistent with the idea that these systems stem from a Creator’s handiwork.

    Still, this recognition does little to dampen the fear and frustration associated with a cancer diagnosis and the pain and suffering experienced by those who battle cancer (and their loved ones who stand on the sidelines watching the fight take place). But, whether we are a skeptic or a believer, we all should be encouraged by the latest insights developed by the Cambridge researchers. The more we understand about the cause and progression of cancers, the closer we are to one day finding cures to a disease that takes so much from us.

    We can also take added encouragement from the powerful scientific case for a Creator’s existence. The Old and New Testaments teach us that the Creator revealed by scientific discovery has suffered on our behalf and will suffer alongside usin the person of Christas we walk through the difficult circumstances of life.

    Resources

    Examples of Biochemical Trade-Offs

    Evidence that Nonfunctional DNA Serves as a Mutational Buffer

    Endnotes
    1. Serena Nik-Zainal and Benjamin A. Hall, “Cellular Survival over Genomic Perfection,” Science 366, no. 6467 (November 15, 2019): 802–03, doi:10.1126/science.aax8046.
    2. Nik-Zainal and Hall, 802–03.
    3. Nik-Zainal and Hall, 802–03.
  • Evolutionary Story Tells the Tale of Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Dec 04, 2019

    In high school I was a bit of a troublemaker. It wasn’t out of the ordinary for me to be summoned to Mr. Reynolds’ office—the school’s vice principal—for some misdeed or other. After a few office visits, I quickly learned the value of a good story. If convincing enough, I could defray the accusations leveled against me. All I had to do was create plausible deniability.

    Story Telling in the Evolutionary Paradigm

    Storytelling isn’t just the purview of a mischievous kid facing the music in the principal’s office, it is part of the construct of science.

    Recent work by a team of scientific investigators from the University of Florida (UF) highlights the central role that storytelling plays in evolutionary biology.1 In fact, it is not uncommon for evolutionary biologists to weave grand narratives that offer plausible evolutionary stories for the emergence of biological or behavioral traits. And, though these accounts seem scientific, they are often unverifiable scientific explanations.

    Inspired by Rudyard Kipling’s (1865–1936) book of children’s origin stories, the late evolutionary biologist Stephen Jay Gould (1941–2002) referred to these evolutionary tales as just-so stories. To be fair, others have been critical of Gould’s cynical view of evolutionary accounts, arguing that, in reality, just-so stories in evolutionary biology are actually hypotheses about evolutionary transformations. But still, more often than not, these “hypotheses” appear to be little more than convenient fictions.

    An Evolutionary Just-So Story of Moths and Bats

    The traditional evolutionary account of ultrasonic sound detection in nocturnal moths serves as a case in point. Moths (and butterflies) belong to one of the most important groups of insects: lepidoptera. This group consists of about 160,000 species, with nocturnal moths comprising over 75 percent of the group.

    Moths play a key role in ecosystems. For example, they serve as one of the primary food sources for bats. Bats use echolocation to help them locate moths at night. Bats emit ultrasonic cries that bounce off the moths and reflect back to the bats, giving these predators the pinpoint location of the moths, even during flight.

    Many nocturnal moth species have defenses that help them escape predation by bats. One defense is ears (located in different areas of their bodies) that detect ultrasonic sounds. This capability allows the moths to hear the bats coming and get out of their way.

    For nearly a half century, evolutionary biologists explained moths’ ability to hear ultrasonic sounds as the outworking of an “evolutionary arms race” between echolocating bats and nocturnal moths. Presumably, bats evolved the ability to echolocate, allowing them to detect and prey upon moths at night by plucking them out of the air in mid-flight. In response, some groups of moths evolved ears that allowed them to detect the ultrasonic screeches emitted by bats, helping them to avoid detection.

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    Figure: Flying Pipistrelle bat. Image credit: Shutterstock

    For 50 years, biologists have studied the relationship between echolocating bats and nocturnal moths with the assumption that this explanation is true. (I doubt Mr. Reynolds ever assumed my stories were true.) In fact, evolutionary accounts like this one provide evidence for the idea of coevolution. Advanced by Paul Ehrlich and Peter Raven in 1964, this evolutionary model maintains that ecosystems are shaped by species that affect one another’s evolution.

    If the UF team’s work is to be believed, then it turns out that the story recounting the evolutionary arms race between nocturnal moths and echolocating bats is fictional. As team member Jesse Barber, a researcher who has studied bats and moths, complains, “Most of the introductions I’ve written in my papers [describing the coevolution of bats and moths] are wrong.”2

    An Evolutionary Study on the Origin of Moths and Butterflies

    To reach this conclusion, the UF team generated the most robust evolutionary tree (phylogeny) for lepidopterans to date. They also developed an understanding of the timing of events in lepidopteran natural history. They were motivated to take on this challenge because of the ecological importance of moths and butterflies. As noted, these insects play a central role in terrestrial ecosystems all over the world and coevolutionary models provide the chief explanations for their place in these ecosystems. But, as the UF researchers note, “These hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking.”3

    To remedy this problem, the researchers built a lepidopteran evolutionary tree from a data set of DNA sequences that collectively specified 2,100 protein-coding genes from 186 lepidopteran species. These species represented all the major divisions within this biological group. Then, they dated the evolutionary timing of key events in lepidopteran natural history from the fossil record.

    Based on their analysis, the research team concluded that the first lepidopteran appeared around 300 million years ago. This creature fed on nonvascular plants. Around 240 million years ago, lepidopterans with tubelike proboscises (long, sucking mouthpiece) appeared, allowing these insects to extract nectar from flowering plants.

    These results cohere with the coevolutionary model that the first lepidopterans fed internally on plants and, later, externally, as they evolved the ability to access nectar from plants. Flowering plants appear around 260 million years ago, which is about the time that the tubelike proboscis appears in lepidopterans.

    But perhaps the most important and stunning finding from their study stems from the appearance of hearing organs in moths. It looks as if these organs arose independently 9 separate times—around 80 to 90 million years ago—well before bats began to echolocate. (The earliest known bat from the fossil record with the capacity to echolocate is around 45 to 50 million years old.)

    The UF investigators uncovered another surprising result related to the appearance of butterflies. They discovered that butterflies became diurnal (active in the daytime) around 98 million years ago. According to the traditional evolutionary story, butterflies (which are diurnal) evolved from nocturnal moths when they transitioned to daytime activities to escape predation of echolocating bats, which feed at night. But as with the origin of hearing organs in moths, the transition from nocturnal to diurnal behavior occurred well before the first appearance of echolocating bats and seems to have occurred independently at least two separate times.

    It Just Isn’t So

    The UF evolutionary biologists’ study demonstrates that the coevolutionary models for the origin of hearing organs in moths and diurnal behavior of butterflies—dominant for over a half century in evolutionary thought—are nothing more than just-so stories. They appear to make sense on the surface but are no closer to the truth than the tales I would weave in Mr. Reynolds’ office.

    In light of this discovery, the research team posits two new evolutionary models for the origin of these two traits, respectively. Now scientists think that the evolutionary emergence of hearing organs in moths may have provided these insects the capacity for auditory surveillance of their environment. Their capacity to hear may have helped them detect the low-frequency sounds of flapping bird wings, for example, and avoid predation. Presumably, these same hearing organs later evolved to detect the high-frequency cries of bats. As for the evolutionary origin of diurnal behavior characteristic of butterflies, researchers now speculate that butterflies became diurnal to take advantage of flowers that bloom in the daytime.

    Again, on the surface, these explanations seem plausible. But one has to wonder if these models, like their predecessors, are little more than just-so stories. In fact, this study raises a general concern: How much confidence can we place in any evolutionary account? Could it be that other evolutionary accounts are, in reality, good stories, but in the end will turn out to be just as fanciful as the stories written by Rudyard Kipling?

    In and of itself, recognizing that many evolutionary models could just be stories doesn’t provide sufficient warrant for skepticism about the evolutionary paradigm. But it does give pause for thought. Plus, two insights from this study raise real concerns about the capacity of evolutionary processes to account for life’s history and diversity:

    1. The discovery that ultrasonic hearing in moths arose independently nine separate times
    2. The discovery that diurnal behavior in butterflies appeared independently in at least two separate instances

    Convergence

    Evolutionary biologists use the term convergence to refer to the independent origin of identical or nearly identical biological and behavioral traits in organisms that cluster into unrelated groups.

    Convergence isn’t a rare phenomenon or limited to the independent origin of hearing organs in moths and diurnal behavior in butterflies. Instead, it is a widespread occurrence in biology, as evolutionary biologists Simon Conway Morris and George McGhee document in their respective books Life’s Solution and Convergent Evolution. It appears as if the evolutionary process routinely arrives at the same outcome, time and time again.4 In fact, biologists observe these repeated outcomes at the ecological, organismal, biochemical, and genetic levels.

    From my perspective, the widespread occurrence of convergent evolution is a feature of biology that evolutionary theory can’t explain. I see the widespread occurrence of convergence as a failed scientific prediction of the evolutionary paradigm.

    Convergence Should Be Rare, Not Widespread

    In effect, chance governs biological and biochemical evolution at its most fundamental level. Evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection, which, too, consists of chance components. The consequences are profound. If evolutionary events could be repeated, the outcome would be dramatically different every time. The inability of evolutionary processes to retrace the same path makes it highly unlikely that the same biological and biochemical designs should appear repeatedly throughout nature.5

    In support of this view, consider a 2002 landmark study carried out by two Canadian investigators who simulated macroevolutionary processes using autonomously replicating computer programs. In their study, the computer programs operated like digital organisms.6 The programs could be placed into different “ecosystems” and, because they replicate autonomously, they could evolve. By monitoring the long-term evolution of these digital organisms, the two researchers determined that evolutionary outcomes are historically contingent and unpredictable. Every time they placed the same digital organism in the same environment, it evolved along a unique trajectory.

    In other words, given the historically contingent nature of the evolutionary mechanisms, we would expect convergence to be rare in the biological realm. Yet, biologists continue to uncover example after example of convergent features—some of which are quite astounding.

    Bat Echolocation and Convergence

    Biologists have discovered one such example of convergence in the origin of echolocating bats. Echolocation appears to have arisen two times independently: once in microbats and once in Rhinolophidae, a superfamily of megabats.7 Prior to this discovery, reported in 2000, biologists classified Rhinolophidae as a microbat based on their capability to echolocate. But DNA evidence indicates that this superfamily has greater affinity to megabats than to microbats. This result means that echolocation must have originated separately in the microbats and Rhinolophidae. Researchers have also shown that the same genetic and biochemical changes occurred in microbats and megabats to create their echolocating ability. These changes appear to have taken place in the gene prestin and in its protein-product, prestin.8

    In other words, we observe two outcomes: (1) the traditional evolutionary accounts for coevolution among echolocating bats, nocturnal moths, and diurnal butterflies turned out to be just-so stories, and (2) the convergence observed in these three groups stands as independent and separate instances of failed predictions of the evolutionary paradigm.

    Convergence and the Case for Creation

    If the widespread occurrence of convergence can’t be explained through evolutionary theory, then how can it be explained?

    It is not unusual for architects and engineers to redeploy the same design features, sometimes in objects, devices, or systems that are completely unrelated to one another. So, instead of viewing convergent features as having emerged through repeated evolutionary outcomes, we could understand them as reflecting the work of a divine mind. From this perspective, the repeated origins of biological features equate to the repeated creations by an intelligent Agent who employs a common set of solutions to address a common set of problems facing unrelated organisms.

    Now that’s a story even Mr. Reynolds might believe.

    Resources

    Convergence of Echolocation

    The Historical Contingency of the Evolutionary Process

    Endnotes
    1. Akito Y. Kawahara et al., “Phylogenomics Reveals the Evolutionary Timing and Pattern of Butterflies and Moths,” Proceedings of the National Academy of Sciences, USA 116, no. 45 (November 5, 2019): 22657–63, doi:10.1073/pnas.1907847116.
    2. Ed Yong, “A Textbook Evolutionary Story about Moths and Bats Is Wrong,” The Atlantic (October 21, 2019), https://www.theatlantic.com/science/archive/2019/10/textbook-evolutionary-story-wrong/600295/.
    3. Kawahara et al., “Phylogenomics.”
    4. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
    5. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1990).
    6. Gabriel Yedid and Graham Bell, “Macroevolution Simulated with Autonomously Replicating Computer Programs,” Nature 420 (December 19, 2002): 810–12, doi:10.1038/nature01151.
    7. Emma C. Teeling et al., “Molecular Evidence Regarding the Origin of Echolocation and Flight in Bats,” Nature 403 (January 13, 2000): 188–92, doi:10.1038/35003188.
    8. Gang Li et al., The Hearing Gene Prestin Reunites Echolocating Bats, Proceedings of the National Academy of Sciences, USA 105, no. 37 (September 16, 2008): 13959–64, doi:10.1073/pnas.0802097105.
  • Evolution of Antibiotic Resistance Makes the Case for a Creator

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Nov 27, 2019

    What would it be like to live in a world without antibiotics?

    It isn’t that hard to imagine, because antibiotics weren’t readily available for medical use until after World War II. And since that time, widespread availability of antibiotics has revolutionized medicine. However, the ability to practice modern medicine is being threatened because of the rise of antibiotic-resistant bacteria. Currently, there exists a pressing need to understand the evolution of antibiotic-resistant strains and to develop new types of antibiotics. Surprisingly, this worthy pursuit has unwittingly stumbled upon evidence for a Creator’s role in the design of biochemical systems.

    Alexander Fleming (1881–1955) discovered the first antibiotic, penicillin, in 1928. But it wasn’t until Ernst Chain, Howard Florey, and Edward Abraham purified penicillin in 1942 and Norman Heatley developed a bulk extraction technique in 1945 that the compound became available for routine medical use.

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    Figure 1: Alexander Fleming. Image Credit: Wikipedia

    Prior to this time, people often died from bacterial infections. Complicating this vulnerability to microbial pathogens was the uncertain outcome of many medical procedures. For example, patients often died after surgery due to complications arising from infections.

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    Figure 2: A generalized structure for penicillin antibiotics. Image credit: Shutterstock

    Bacterial Resistance Necessitates New Antibiotics

    Unfortunately, because of the growing threat of superbugs—antibiotic-resistant strains of bacteria—health experts around the world worry that we soon will enter into a post-antibiotic era in which modern medicine will largely revert to pre-World War II practices. According to Dr. David Livermore, laboratory director at Public Health England, which is responsible for monitoring antibiotic-resistant strains of bacteria, “A lot of modern medicine would become impossible if we lost our ability to treat infections.”1

    Without antibiotics, people would routinely die of infections that we easily treat today. Abdominal surgeries would be incredibly risky. Organ transplants and chemotherapy would be out of the question. And the list continues.

    The threat of entering into a post-antibiotic age highlights the desperate need to develop new types of antibiotics. It also highlights the need to develop a better understanding of evolutionary processes that lead to the emergence of antibiotic resistance in bacteria.

    Recently, a research team from Michigan State University (MSU) published a report that offers insight into the latter concern. These researchers studied the evolution of antibiotic resistance in bacteria that had been serially cultured in the laboratory for multiple decades in media that was free from antibiotics.2 Through this effort, they learned that the genetic history of the bacterial strain plays a key role in its acquisition of resistance to antibiotics.

    This work has important implications for public health, but it also carries theological implications. The decades-long experiment provides evidence that the elegant designs characteristic of biochemical and biological systems most likely stem from a Creator’s handiwork.

    The Long-Term Evolution Experiment

    To gain insight into the role that genetic history plays in the evolution of antibiotic resistance, the MSU researchers piggy-backed on the famous Long-Term Evolution Experiment (LTEE) at Michigan State University. Inaugurated in 1988, the LTEE is designed to monitor evolutionary changes in the bacterium E. coli, with the objective of developing an understanding of the evolutionary process.

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    Figure 3: A depiction of E. coli. Image Credit: Shutterstock

    The LTEE began with a single cell of E. coli that was used to generate twelve genetically identical lines of cells. The twelve clones of the parent E. coli cell were separately inoculated into a minimal growth medium containing low levels of glucose as the only carbon source. After growing overnight, an aliquot (equal fractional part) of each of the twelve cultures was transferred into fresh growth media. This process has been repeated every day for about thirty years. Throughout the experiment, aliquots of cells have been frozen every 500 generations. These frozen cells represent a “fossil record” of sorts that can be thawed out and compared to current and other past generations of cells.

    Relaxed Selection and Decay of Antibiotic Resistance

    In general, when a population of organisms no longer experiences natural selection for a particular set of traits (antibiotic resistance, in this case), the traits designed to handle that pressure may experience functional decay as a result of mutations and genetic drift. This process is called relaxed selection.

    In the case of antibiotic resistance, when the threat of antibiotics is removed from the population (relaxed selection), it seems reasonable to think that antibiotic resistance would decline in the population because in most cases antibiotic resistance comes with a fitness cost. In other words, bacterial strains that acquire antibiotic resistance face a trade-off that makes them less fit in environments without the antibiotic.

    Genetic History and the Re-Evolution of Antibiotic Resistance

    In light of this expectation, the MSU researchers wondered how readily bacteria that have experienced relaxed selection can overcome loss of antibiotic resistance when the antibiotic is reintroduced to the population.

    To explore this question, the researchers examined the evolution of antibiotic resistance in the LTEE ancestor by exposing it to a set of different antibiotics and compared its propensity to acquire antibiotic resistance with four strains of E. coli derived from the LTEE ancestor (that underwent 50,000 generations of daily growth and transfer into fresh media in the absence of exposure to antibiotics).

    As expected, the MSU team discovered that 50,000 generations of relaxed selection rendered the four strains more susceptible to four different antibiotics (ampicillin, ceftriaxone, ciprofloxacin, and tetracycline) compared to the LTEE ancestor. When they exposed these strains to the different antibiotics, the researchers discovered that acquisition of antibiotic resistance was idiosyncratic: some strains more readily evolved antibiotic resistance than the LTEE ancestor and others were less evolvable.

    Investigators explained this difference by arguing that during the period of relaxed selection some of the strains experienced mutations that constrained the evolution of antibiotic resistance, whereas others experienced mutations that potentiated (activated) the evolution of antibiotic resistance. That is, historical contingency has played a key role in the acquisition of antibiotic resistance. Different bacterial lineages accumulated genetic differences that influence their capacity to evolve and adapt in new directions.

    Historical Contingency

    This study follows on the heels of previous studies that demonstrate the historical contingency of the evolutionary process.3 In other words, chance governs biological and biochemical evolution at its most fundamental level. As the MSU researchers observed, evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection (or that experience relaxed selection), which, too, consists of chance components.

    Because of the historically contingent nature of the evolutionary process, it is highly unlikely that the same biological and biochemical designs should appear repeatedly throughout nature. In his book Wonderful Life, Stephen Jay Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.4

    The “Problem” of Convergence

    And yet, we observe the opposite pattern in biology. From an evolutionary perspective, it appears as if the evolutionary process independently and repeatedly arrived at the same outcome, time and time again (convergence). As evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books Life’s Solution and Convergent Evolution, identical evolutionary outcomes are a widespread feature of the biological realm.5

    Scientists see these repeated outcomes at ecological, organismal, biochemical, and genetic levels. To illustrate the pervasiveness of convergence at the biochemical level, I describe 100 examples of convergence in my book The Cell’s Design.6

    From my perspective, the widespread occurrence of convergent evolution is a feature of biology that evolutionary theory can’t genuinely explain. In fact, given the clear-cut demonstration that the evolutionary process is historically contingent, I see the widespread occurrence of convergence as a failed scientific prediction for the evolutionary paradigm.

     

    Evolution in Bacteria Doesn’t Equate to Large-Scale Evolution

    The evolution of E. coli in the LTEE doesn’t necessarily validate the evolutionary paradigm. Just because such change is observed in a microbe doesn’t mean that evolutionary processes can adequately account for life’s origin and history, and the full range of biodiversity.

     

    Convergence and the Case for Creation

    Instead of viewing convergent features as having emerged through repeated evolutionary outcomes, we could understand them as reflecting the work of a divine Mind. In this scheme, the repeated origins of biological features equate to the repeated creations by an intelligent Agent who employs a common set of solutions to address a common set of problems facing unrelated organisms.

    Sadly, many in the scientific community are hesitant to embrace this perspective because they are resistant to the idea that design and purpose may play a role in biology. But, one can hope that someday the scientific community will be willing to move into a post-evolution future as the evidence for a Creator’s role in biology mounts.

    Resources

    The Historical Contingency of the Evolutionary Process

    Microbial Evolution and the Validity of the Evolutionary Paradigm

    Endnotes
    1. Sarah Bosley, “Are You Ready for a World without Antibiotics?” The Guardian, August 12, 2010, https://www.theguardian.com/society/2010/aug/12/the-end-of-antibiotics-health-infections.
    2. Kyle J. Card et al., “Historical Contingency in the Evolution of Antibiotic Resistance after Decades of Relaxed Selection,” PLoS Biology 17, no. 10 (October 23, 2019): e3000397, doi:10.1371/journal.pbio.3000397.
    3. Zachary D. Blount et al., “Historical Contingency and the Evolution of a Key Innovation in an Experimental Population of Escherichia coli,” Proceedings of the National Academy of Sciences USA 105, no. 23 (June 10, 2008): 7899-7906, doi:10.1073/pnas.0803151105.
    4. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W.W. Norton & Company, 1990).
    5. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
    6. Fazale Rana, The Cell’s Design: How Chemistry Reveal the Creator’s Artistry (Grand Rapids, MI: Baker, 2008).
  • Analysis of Genomes Converges on the Case for a Creator

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Nov 13, 2019

    Are you a Marvel or a DC fan?

    Do you like the Marvel superheroes better than those who occupy the DC universe? Or is it the other way around for you?

    Even though you might prefer DC over Marvel (or Marvel over DC), over the years these two comic book rivals have often created superheroes with nearly identical powers. In fact, a number of Marvel and DC superheroes are so strikingly similar that their likeness to one another is obviously intentional.1

    Here are just a few of the superheroes Marvel and DC have ripped off each other:

    • Superman (DC, created in 1938) and Hyperion (Marvel, created in 1969)
    • Batman (DC, created in 1939) and Moon Knight (Marvel, created in 1975)
    • Green Lantern (DC, created in 1940) and Nova (Marvel, created in 1976)
    • Catwoman (DC, created in 1940) and Black Cat (Marvel, created in 1979)
    • Atom (DC, created in 1961) and Ant-Man (Marvel, created in 1962)
    • Aquaman (DC, created in 1941) and Namor (Marvel, created in 1939)
    • Green Arrow (DC, created in 1941) and Hawkeye (Marvel, created in 1964)
    • Swamp Thing (DC, created in 1971) and Man Thing (Marvel, created in 1971)
    • Deathstroke (DC, created in 1980) and Deadpool (Marvel, created in 1991)

    This same type of striking similarity is also found in biology. Life scientists have discovered countless examples of biological designs that are virtually exact replicas of one another. Yet, these identical (or nearly identical) designs occur in organisms that belong to distinct, unrelated groups (such as the camera eyes of vertebrates and octopi). Therefore, they must have an independent origin.

     

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    Figure 1: The Camera Eyes of Vertebrates (left) and Cephalopods (right); 1: Retina; 2: Nerve Fibers; 3: Optic Nerve; 4: Blind Spot. Image credit: Wikipedia

    From an evolutionary perspective, it appears as if the evolutionary process independently and repeatedly arrived at the same outcome, time and time again. As evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books, Life’s Solution and Convergent Evolution, identical evolutionary outcomes are a widespread feature of the biological realm.2 Scientists observe these repeated outcomes (known as convergence) at the ecological, organismal, biochemical, and genetic levels.

    From my perspective, the widespread occurrence of convergent evolution is a feature of biology that evolutionary theory can’t genuinely explain. In fact, I see pervasive convergence as a failed scientific prediction—for the evolutionary paradigm. Recent work by a research team from Stanford University demonstrates my point.3

    These researchers discovered that identical genetic changes occurred when: (1) bats and whales “evolved” echolocation, (2) killer whales and manatees “evolved” specialized skin in support of their aquatic lifestyles, and (3) pikas and alpacas “evolved” increased lung capacity required to live in high-altitude environments.

    Why do I think this discovery is so problematic for the evolutionary paradigm? To understand my concern, we first need to consider the nature of the evolutionary process.

    Biological Evolution Is Historically Contingent

    Essentially, chance governs biological and biochemical evolution at its most fundamental level. Evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection, which, too, consists of chance components. The consequences are profound. If evolutionary events could be repeated, the outcome would be dramatically different every time. The inability of evolutionary processes to retrace the same path makes it highly unlikely that the same biological and biochemical designs should appear repeatedly throughout nature.

    The concept of historical contingency embodies this idea and is the theme of Stephen Jay Gould’s book Wonderful Life.4 To help illustrate the concept, Gould uses the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

    Are Evolutionary Processes Historically Contingent?

    Gould based the concept of historical contingency on his understanding of the evolutionary process. In the decades since Gould’s original description of historical contingency, several studies have affirmed his view.

    For example, in a landmark study in 2002, two Canadian investigators simulated macroevolutionary processes using autonomously replicating computer programs, with the programs operating like digital organisms.5 These programs were placed into different “ecosystems” and, because they replicated autonomously, could evolve. By monitoring the long-term evolution of the digital organisms, the two researchers determined that evolutionary outcomes are historically contingent and unpredictable. Every time they placed the same digital organism in the same environment, it evolved along a unique trajectory.

    In other words, given the historically contingent nature of the evolutionary mechanisms, we would expect convergence to be rare in the biological realm. Yet, biologists continue to uncover example after example of convergent features—some of which are quite astounding.

    The Origin of Echolocation

    One of the most remarkable examples of convergence is the independent origin of echolocation (sound waves emitted from an organism to an object and then back to the organism) in bats (chiropterans) and cetaceans (toothed whales). Research indicates that echolocation arose independently in two different groups of bats and also in the toothed whales.

     

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    Figure 2: Echolocation in Bats. Image credit: Shutterstock

    One reason why this example of convergence is so remarkable has to do with the way some evolutionary biologists account for the widespread occurrences of convergence in biological systems. Undaunted by the myriad examples of convergence, these scientists assert that independent evolutionary outcomes result when unrelated organisms encounter nearly identical selection forces (e.g., environmental, competitive, and predatory pressures). According to this idea, natural selection channels unrelated organisms down similar pathways toward the same endpoint.

    But this explanation is unsatisfactory because bats and whales live in different types of habitats (terrestrial and aquatic). Consequently, the genetic changes responsible for the independent emergence of echolocation in the chiropterans and cetaceans should be distinct. Presumably, the evolutionary pathways that converged on a complex biological system such as echolocation would have taken different routes that would be reflected in the genomes. In other words, even though the physical traits appear to be identical (or nearly identical), the genetic makeup of the organisms should reflect an independent evolutionary history.

    But this expectation isn’t borne out by the data.

    Genetic Convergence Parallels Trait Convergence

    In recent years, evolutionary biologists have developed interest in understanding the genetic basis for convergence. Specifically, these scientists want to understand the genetic changes that lead to convergent anatomical and physiological features (how genotype leads to phenotype).

    Toward this end, a Stanford research team developed an algorithm that allowed them to search through entire genome sequences of animals to identify similar genetic features that contribute to particular biological traits.6 In turn, they applied this method to three test cases related to the convergence of:

    • echolocation in bats and whales
    • scaly skin in killer whales
    • lung structure and capacity in pikas and alpacas

    The investigators discovered that for echolocating animals, the same 25 convergent genetic changes took place in their genomes and were distributed among the same 18 genes. As it turns out, these genes play a role in the development of the cochlear ganglion, thought to be involved in echolocation. They also discovered that for aquatic mammals, there were 27 identical convergent genetic changes that occurred in same 15 genes that play a role in skin development. And finally, for high-altitude animals, they learned that the same 25 convergent genetic changes occurred in the same 16 genes that play a role in lung development.

    In response to this finding, study author Gill Bejerano remarked, “These genes often control multiple functions in different tissues throughout the body, so it seems it would be very difficult to introduce even minor changes. But here we’ve found that not only do these very different species share specific genetic changes, but also that these changes occur in coding genes.”7

    In other words, these results are not expected from an evolutionary standpoint. It is nothing short of amazing that genetic convergence would parallel phenotypic convergence.

    On the other hand, these results make perfect sense from a creation model vantage point.

    Convergence and the Case for Creation

    Instead of viewing convergent features as having emerged through repeated evolutionary outcomes, we could understand them as reflecting the work of a Divine Mind. In this scheme, the repeated origins of biological features equate to the repeated creations by an Intelligent Agent who employs a common set of solutions to address a common set of problems facing unrelated organisms.

    Like the superhero rip-offs in the Marvel and DC comics, the convergent features in biology appear to be intentional, reflecting a teleology that appears to be endemic in living systems.

    Resources

    Convergence of Echolocation

    The Historical Contingency of the Evolutionary Process

    Endnotes
    1. Jamie Gerber, 15 DC and Marvel Superheroes Who Are Strikingly Similar, ScreenRant (November 12, 2016), screenrant.com/marvel-dc-superheroes-copies-rip-offs/.
    2. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
    3. Amir Marcovitz et al., “A Functional Enrichment Test for Molecular Convergent Evolution Finds a Clear Protein-Coding Signal in Echolocating Bats and Whales,” Proceedings of the National Academy of Sciences, USA 116, no. 42 (October 15, 2019), 21094–21103, doi:10.1073/pnas.1818532116.
    4. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1990).
    5. Gabriel Yedid and Graham Bell, “Macroevolution Simulated with Autonomously Replicating Computer Programs,” Nature 420 (December 19, 2002): 810–12, doi:10.1038/nature01151.
    6. Marcovitz et al., “A Functional Enrichment Test.”
    7. Stanford Medicine, “Scientists Uncover Genetic Similarities among Species That Use Sound to Navigate,” ScienceDaily, October 4, 2019, sciencedaily.com/releases/2019/10/191004105643.htm.
  • Glue Production Is Not Evidence for Neanderthal Exceptionalism

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Nov 06, 2019

    Football players aren’t dumb jocks—though they often have that reputation. Football is a physically demanding sport that requires strength, toughness, agility, and speed. But it is also an intellectually demanding game.

    Mastering a playbook, understanding which plays work best for the various in-game scenarios, recognizing defenses and offenses, and adjusting on the fly require hours of study and preparation. Football really is a thinking person’s game.

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    Figure 1: Quarterback Calling an Audible at the Line of Scrimmage. Image Credit: Shutterstock

    Some anthropologists view Neanderthals in the same way that many people view football players: as the “dumb jock” version of a hominin, a creature cognitively inferior to modern humans. Yet, other anthropologists dispute this characterization, arguing that it is undeserved. Instead, they claim that Neanderthals had cognitive capabilities on par with modern humans.

    In support of their claim, these scientists point to finds in the archaeological record that seemingly suggest these hominins were exceptional, just like modern humans. As a case in point, archaeologists have unearthed evidence for tar production at a site in Italy that dates to around 200,000 years in age. They interpret this discovery as evidence that Neanderthals were using tar as glue for hafting (fixing) flint spearheads to wooden spear shafts.1 Archaeologists have also unearthed spearheads with tar residue from two sites in Germany, one dating to 120,000 years in age and the other between 40,000 to 80,000 years.2 Because these dates precede the arrival of modern humans into Europe, anthropologists assume the tar at these sites was deliberately produced and used by Neanderthals.

    Adhesives as a Signature for Superior Cognition

    Anthropologists consider the development of adhesives as a transformative technology. These materials would have provided the first humans the means to construct new types of complex devices and combine different types of materials (composites) into new technologies. Because of this new proficiency, anthropologists consider the production and use of adhesives to be diagnostic of advanced cognitive capabilities such as forward planning, abstraction, and understanding of materials.

    Production of adhesives from natural sources, even by the earliest modern humans, appears to have been a complex operation that required precise temperature control and the use of earthen mounds, or ceramic or metal kilns. In addition, birch bark needed to be heated in the absence of oxygen. Because the first large-scale production of adhesives usually centered around the dry distillation of birch and pine barks to produce tar and pitch, researchers have assumed that this technique is the only way to generate tar.

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    Figure 2: Tar Produced from Birch Bark. Image credit: Wikipedia

    So, if Neanderthals were using tar as an adhesive, the reasoning goes, they must have been pretty impressive creatures.

    In the summer of 2017 researchers from the University of Leiden published work that seemed to support this view.3 To address the question of how Neanderthals may have produced adhesives, these investigators conducted a series of experiments. They sought to learn how Neanderthals used the resources most reasonably available to them to obtain tar from birch bark through dry distillation.

    By studying a variety of methods for dry distillation of tar from birch in a laboratory setting, the research team concluded that Neanderthals could have produced tar from birch bark if they had used methods that were simple enough that they wouldn’t require precise temperature control during the distillation. Still, these methods are complex enough that the researchers concluded that for Neanderthals to pull off this feat, they must have had advanced cognitive abilities similar to those of modern humans.

    Is Adhesive Production and Use Evidence for Neanderthal Exceptionalism?

    At the time this work was reported, I challenged this conclusion by noting that the simplicity of these production methods argued against advanced cognitive abilities in Neanderthals, not for them.

    Recent work by researchers from Germany affirms my skepticism. Their research challenges the view that adhesive production and use constitutes evidence for human exceptionalism.4 The team wondered if a simpler way to produce tar—even simpler than the methods identified by the research team from the University of Leiden— exists. They also wondered if it was possible to produce tar in the presence of oxygen.

    From their work, they discovered that burning birch bark (or branches from a birch tree with the bark still attached) adjacent to a rock with a vertical or subvertical surface is a way to collect tar, which naturally deposits on the rock surface as the bark burns. In other words, tar can be produced accidentally, instead of deliberately. And once produced, it can be scraped from the rock surface.

    Using analytical techniques (gas chromatography coupled to mass spectrometry) to characterize the chemical makeup of the tar produced by this simple method, the research team showed that it is comparable to the chemical composition of tars produced by sophisticated dry distillation methods under anaerobic conditions. Because of the simplicity of this method, the research team thinks that collecting tar deposits from burning birch on rocks is the most likely way that Neanderthals produced tar, if they intentionally produced it at all.

    According to the research team, “The identification of birch tar at archaeological sites can no longer be considered as a proxy for human (complex, cultural) behavior as previously assumed. In other words, our finding changes textbook thinking about what tar production is a smoking gun of.”5

    One other point merits consideration: A growing body of evidence indicates that Neanderthals did not master fire, but rather used it opportunistically. In other words, these creatures could not create fire, but did harvest wildfires. Evidence demonstrates that there were vast periods of time during Neanderthals’ tenure in Europe when wildfires were rare because of cold climatic conditions. During these periods, Neanderthals didn’t use fire.

    Because fire is central to the dry distillation methods, for a significant portion of their time on Earth Neanderthals would have been unable to extract tar and use it for hafting. Perhaps this factor explains why recovery of tar from Neanderthal sites is so rare. And could it be that Neanderthals were not intentionally producing tar? Instead, did tar just happen to collect on rock surfaces as a consequence of burning birch branches when these creatures were able to harvest fire?

    What Difference Does It Make?

    One of the most important ideas taught in Scripture is that human beings uniquely bear God’s image. As such, every human being has immeasurable worth and value. And because we bear God’s image, we can enter into a relationship with our Maker.

    However, if Neanderthals possessed advanced cognitive ability just like that of modern humans, then it becomes difficult to maintain the view that modern humans are unique and exceptional. If human beings aren’t exceptional, then it becomes a challenge to defend the idea that human beings are made in God’s image.

    Yet, claims that Neanderthals are cognitive equals to modern humans fail to withstand scientific scrutiny, time and time again, as this latest study demonstrates. It is unlikely that any of us will see a Neanderthal run onto the football field anytime soon.

    Resources

    Neanderthals Did Not Master Fire

    Differences in Human and Neanderthal Brains

    Endnotes
    1. Paul Peter Anthony Mazza et al., “A New Palaeolithic Discovery: Tar-Hafted Stone Tools in a European Mid-Pleistocene Bone-Bearing Bed,” Journal of Archaeological Science 33, no. 9 (September 2006): 1310–18, doi:10.1016/j.jas.2006.01.006.
    2. Johann Koller, Ursula Baumer, and Dietrich Mania, “High-Tech in the Middle Palaeolithic: Neandertal-Manufactured Pitch Identified,” European Journal of Archaeology 4, no. 3 (December 1, 2001): 385–97, doi:10.1179/eja.2001.4.3.385; Alfred F. Pawlik and Jürgen P. Thissen, “Hafted Armatures and Multi-Component Tool Design at the Micoquian Site of Inden-Altdorf, Germany,” Journal of Archaeological Science 38, no. 7 (July 2011): 1699–1708, doi:10.1016/j.jas.2011.03.001.
    3. P. R. B. Kozowyk et al., “Experimental Methods for the Palaeolithic Dry Distillation of Birch Bark: Implications for the Origin and Development of Neandertal Adhesive Technology,” Scientific Reports 7 (August 31, 2017): 8033, doi:10.1038/s41598-017-08106-7.
    4. Patrick Schmidt et al., “Birch Tar Production Does Not Prove Neanderthal Behavioral Complexity,” Proceedings of the National Academy of Sciences, USA 116, no. 36 (September 3, 2019): 17707–11, doi:10.1073/pnas.1911137116.
    5. Schmidt et al., “Birch Tar Production.”
  • Scientists Reverse the Aging Process: Exploring the Theological Implications

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Oct 30, 2019

    During those days people will seek death but will not find it; they will long to die, but death will elude them.

    Revelation 9:6

     

    I make dad noises now.

    When I sit down, when I stand up, when I get out of bed, when I get into bed, when I bend over to pick up something from the ground, and when I straighten up again, I find myself involuntarily making noises—grunting sounds.

    I guess it is all part of the aging process. My body isn’t quite what it used to be. If someone offered me an elixir that could turn back time and reverse the aging process, I would take it without hesitation. It’s no fun growing old.

    Well, I just might get my wish, thanks to the work of a research team from the US and Canada. These researchers demonstrated that they could disrupt the aging process and, in fact, reverse the biological clock in humans.1

    This advance is nothing short of stunning. It opens up exciting—and disquieting—biomedical possibilities rife with ethical and theological ramifications. The work has other interesting implications, as well. It can be marshaled to demonstrate the scientific credibility of the Old Testament by making scientific sense of the long life spans of the patriarchs listed in the Genesis 5 and 11 genealogies.

    Some Biological Consequences of Aging

    Involuntary grunting is not the worse part of aging, by far. There are other more serious consequences, such as loss of immune function. Senescence (aging) of the immune system can contribute to the onset of cancer and increased susceptibility to pathogens. It can also lead to wide-scale inflammation. None of these are good.

    As we age, our thymus decreases in size. And this size reduction hampers immune system function. Situated between the heart and sternum, the thymus plays a role in maturation of white blood cells, key components of the immune system. As the thymus shrinks with age, the immune system loses its capacity to generate sufficient levels of white blood cells, rendering older adults vulnerable to infections and cancers.

    A Strategy to Improve Immune Function

    Previous studies in laboratory animals have shown that administering growth hormone enlarges the thymus and, consequently, improves immune function. The research team reasoned that the same effect would be seen in human patients. But due to at least one of its negative side effects, the team couldn’t simply administer growth hormone without other considerations. Growth hormone lowers insulin levels and leads to a form of type 2 diabetes. To prevent this adverse effect, the researchers also administered two drugs commonly used to treat type 2 diabetes.

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    Figure 1: The Structure of Human Growth Hormone. Image credit: Shutterstock

    To test this idea, the researchers performed a small-scale clinical trial. The study began with ten men (finishing with nine) between the ages of 51 and 65. The volunteers self-administered the drug cocktail three to four times a week for a year. During the course of the study, the researchers monitored white blood cell levels and thymus size. They observed a rejuvenation of the immune system (based on the count of white blood cells in the blood). They also noticed changes in the thymus, with fatty deposits disappearing and thymus tissue returning.

    Reversing the Aging Process

    As an afterthought, the researchers decided to test the patient’s blood using an epigenetic clock that measures biological age. To their surprise, the researchers discovered that the drug cocktail reversed the biological age of the study participants by two years, compared to their chronological age. In other words, even though the patients gained one year in their chronological age during the course of the study, their bodies became younger, based on biological markers, by two years. This age reversal lasted for six months after the trial ended.

    Thus, for the first time ever, researchers have been able to extend human life expectancy through an aging-intervention therapy. And while the increase in life expectancy was limited, this accomplishment serves as a harbinger of things to come, making the prospects of dramatically extending human life expectancy significantly closer to a reality.

    This groundbreaking work carries significant biomedical, ethical, and theological implications, which I will address below. But the breakthrough is equally fascinating to me because it can be used to garner scientific support for Genesis 5 and 11.

    Anti-Aging Technology and Biblical Long Life Spans

    The mere assertion that humans could live for hundreds of years as described in the genealogies of Genesis 5 and 11 is, for many people, nothing short of absurd. Compounding this seeming absurdity is the claim in Genesis 6:3, which describes God intervening to shorten human life spans from about 900 to about 120 years. How can this dramatic change in human life spans be scientifically rational?

    As I discuss in Who Was Adam?, advances in the biochemistry of aging provide a response to these challenging questions. Scientists have uncovered several distinct biochemical mechanisms that either cause, or are associated with, senescence. Even subtle changes in cellular chemistry can increase life expectancy by nearly 50 percent. These discoveries point to several possible ways that God could have allowed long life spans and then altered human life expectancy—simply by “tweaking” human biochemistry.

    Thanks to these advances, biogerontologists have become confident that in the near future, they will be able to interrupt the aging process by direct intervention through altered diet, drug treatment, and gene manipulation. Some biogerontologists such as Aubrey de Grey don’t think it is out of the realm of possibility to extend human life expectancy to several hundred years—about the length of time the Bible claims that the patriarchs lived. The recent study by the US and Canadian investigators seems to validate de Grey’s view.

    So, if biogerontologists can alter life spans—maybe someday on the order of hundreds of years—then the Genesis 5 and 11 genealogies no longer appear to be fantastical. And, if we can intervene in our own biology to alter life spans, how much easier must it be for God to do so?

    Ethical Concerns

    As mentioned, I would be tempted to take an anti-aging elixir if I knew it would work. And so would many others. What could possibly be wrong with wanting to live a longer, healthier, and more productive life? In fact, disrupting—and even reversing—the aging process would offer benefits to society by potentially reducing medical costs associated with age-related diseases such as dementia, cancer, heart disease, and stroke.

    Yet, these biomedical advances in anti-aging therapies do hold the potential to change who we are as human beings. Even a brief moment of reflection makes it plain that wide-scale use of anti-aging treatments could bring about fundamental changes to economies, to society, and to families and put demands on limited planetary resources. In the end, anti-aging technologies may well be unsustainable, undesirable, and unwise. (For a more detailed discussion of the ethical issues surrounding anti-aging technology check out the book I cowrote with Kenneth Samples, Humans 2.0.)

    Anti-Aging Therapies and Transhumanism

    Many people rightly recognize the ethical concerns surrounding applications of anti-aging therapies, but a growing number see these technologies in a different light. They view them as paving the way to an exciting and hopeful future. The increasingly real prospects of extending human life expectancy by disrupting the aging process or even reversing the effects of aging are the types of advances (along with breakthroughs in CRISPR gene editing and computer-brain interfaces) that fuel an intellectual movement called transhumanism.

    This idea has long been on the fringes of respected academic thought, but recently transhumanism has propelled its way into the scientific, philosophical, and cultural mainstreams. Advocates of the transhumanist vision maintain that humanity has an obligation to use advances in biotechnology and bioengineering to correct our biological flaws—to augment our physical, intellectual, and psychological capabilities beyond our natural limits. Perhaps there are no greater biological limitations that human beings experience than those caused by aging bodies and the diseases associated with the aging process.

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    Figure 2: Transhumanism. Image credit: Shutterstock

    Transhumanists see science and technology as the means to alleviate pain and suffering and to promote human flourishing. They note, in the case of aging, the pain, suffering, and loss associated with senescence in human beings. But the biotechnology we need to fulfill the transhumanist vision is now within grasp.

    Anti-Aging as a Source of Hope and Salvation?

    Using science and technology to mitigate pain and suffering and to drive human progress is nothing new. But transhumanists desire more. They advocate that we should use advances in biotechnology and bioengineering for the self-directed evolution of our species. They seek to fulfill the grand vision of creating new and improved versions of human beings and ushering in a posthuman future. In effect, transhumanists desire to create a utopia of our own design.

    In fact, many transhumanists go one step further, arguing that advances in gene editing, computer-brain interfaces, and anti-aging technologies could extend our life expectancy, perhaps even indefinitely, and allow us to attain a practical immortality. In this way, transhumanism displays its religious element. Here science and technology serve as the means for salvation.

    Transhumanism: a False Gospel?

    But can transhumanism truly deliver on its promises of a utopian future and practical immortality?

    In Humans 2.0, Kenneth Samples and I delineate a number of reasons why transhumanism is a false gospel, destined to disappoint, not fulfill, our desire for immortality and utopia. I won’t elaborate on those reasons here. But simply recognizing the many ethical concerns surrounding anti-aging technologies (and gene editing and computer-brain interfaces) highlights the real risks connected to pursuing a transhumanist future. If we don’t carefully consider these concerns, we might create a dystopian future, not a utopian world.

    The mere risk of this type of unintended future should give us pause for thought about turning to science and technology for our salvation. As theologian Ronald Cole-Turner so aptly put it:

    “We need to be aware that technology, precisely because of its beneficial power, can lead us to the erroneous notion that the only problems to which it is worth paying attention involve engineering. When we let this happen, we reduce human yearning for salvation to a mere desire for enhancement, a lesser salvation that we can control rather than the true salvation for which we must also wait.”2

    Resources

    Endnotes
    1. Gregory M. Fahy et al., “Reversal of Epigenetic Aging and Immunosenescent Trends in Humans,” Aging Cell (September 8, 2019): e13028, doi:10.1111/acel.13028.
    2. “Transhumanism and Christianity,” in Transhumanism and Transcendence: Christian Hope in an Age of Technological Enhancement, ed. Ronald Cole-Turner (Washington, D.C.: Georgetown University Press, 2011), 201.
  • Origin and Design of the Genetic Code: A One-Two Punch for Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Oct 23, 2019

    True confession: I am a sports talk junkie. It has gotten so bad that sometimes I would rather listen to people talk about the big game than actually watch it on TV.

    So, in the spirit of the endless debates that take place on sports talk radio, I ask: What duo is the greatest one-two punch in NBA history? Is it:

    • Kareem and Magic?
    • Kobe and Shaq?
    • Michael and Scottie?

    Another confession: I am a science-faith junkie. I never tire when it comes to engaging in discussions about the interplay between science and the Christian faith. From my perspective, the most interesting facet of this conversation centers around the scientific evidence for God’s existence.

    So, toward this end, I ask: What is the most compelling biochemical evidence for God’s existence? Is it:

    • The complexity of biochemical systems?
    • The eerie similarity between biomolecular motors and machines designed by human engineers?
    • The information found in DNA?

    Without hesitation I would say it is actually another feature: the origin and design of the genetic code.

    The genetic code is a biochemical code that consists of a set of rules defining the information stored in DNA. These rules specify the sequence of amino acids used by the cell’s machinery to synthesize proteins. The genetic code makes it possible for the biochemical apparatus in the cell to convert the information formatted as nucleotide sequences in DNA into information formatted as amino acid sequences in proteins.

     

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    Figure: A Depiction of the Genetic Code. Image credit: Shutterstock

    In previous articles (see the Resources section), I discussed the code’s most salient feature that I think points to a Creator’s handiwork: it’s multidimensional optimization. That optimization is so extensive that evolutionary biologists struggle to account for it’s origin, as illustrated by the work of biologist Steven Massey1.

    Both the optimization of the genetic code and the failure of evolutionary processes to account for its design form a potent one-two punch, evincing the work of a Creator. Optimization is a marker of design, and if it can’t be accounted for through evolutionary processes, the design must be authentic—the product of a Mind.

    Can Evolutionary Processes Generate the Genetic Code?

    For biochemists working to understand the origin of the genetic code, its extreme optimization means that it is not the “frozen accident” that Francis Crick proposed in a classic paper titled “On the Origin of the Genetic Code.”2

    Many investigators now think that natural selection shaped the genetic code, producing its optimal properties. However, I question if natural selection could evolve a genetic code with the degree of optimality displayed in nature. In the Cell’s Design (published in 2008), I cite the work of the late biophysicist Hubert Yockey in support of my claim.3 Yockey determined that natural selection would have to explore 1.40 x 1070 different genetic codes to discover the universal genetic code found in nature. Yockey estimated 6.3 x 1015 seconds (200 million years) is the maximum time available for the code to originate. Natural selection would have to evaluate roughly 1055 codes per second to find the universal genetic code. And even if the search time was extended for the entire duration of the universe’s existence, it still would require searching through 1052 codes per second to find nature’s genetic code. Put simply, natural selection lacks the time to find the universal genetic code.

    Researchers from Germany raised the same difficulty for evolution recently. Because of the genetic code’s multidimensional optimality, they concluded that “the optimality of the SGC [standard genetic code] is a robust feature and cannot be explained by any simple evolutionary hypothesis proposed so far. . . . the probability of finding the standard genetic code by chance is very low. Selection is not an omnipotent force, so this raises the question of whether a selection process could have found the SGC in the case of extreme code optimalities.”4

    Two More Evolutionary Mechanisms Considered

    Life scientist Massey reached a similar conclusion through a detailed analysis of two possible evolutionary mechanisms, both based on natural selection.9

    If the genetic code evolved, then alternate genetic codes would have to have been generated and evaluated until the optimal genetic code found in nature was discovered. This process would require that coding assignments change. Biochemists have identified two mechanisms that could contribute to coding reassignments: (1) codon capture and (2) an ambiguous intermediate mechanism. Massey tested both mechanisms.

    Massey discovered that neither mechanism can evolve the optimal genetic code. When he ran computer simulations of the evolutionary process using codon capture as a mechanism, they all ended in failure, unable to find a highly optimized genetic code. When Massey ran simulations with the ambiguous intermediate mechanism, he could evolve an optimized genetic code. But he didn’t view this result as success. He learned that it takes between 20 to 30 codon reassignments to produce a genetic code with the same degree of optimization as the genetic code found in nature.

    The problem with this evolutionary mechanism is that the number of coding reassignments observed in nature is scarce based on the few deviants of the genetic code thought to have evolved since the origin of the last common ancestor. On top of this problem, the structure of the optimized codes that evolved via the ambiguous intermediate mechanism is different from the structure of the genetic code found in nature. In short, the result obtained via the ambiguous intermediate mechanism is unrealistic.

    As Massey points out, “The evolution of the SGC remains to be deciphered, and constitutes one of the greatest challenges in the field of molecular evolution.”10

    Making Sense of Explanatory Models

    In the face of these discouraging results for the evolutionary paradigm, Massey concludes that perhaps another evolutionary force apart from natural selection shaped the genetic code. One idea Massey thinks has merit is the Coevolution Theory proposed by J. T. Wong. Wong argued that the genetic code evolved in conjunction with the evolution of biosynthetic pathways that produce amino acids. Yet, Wong’s theory doesn’t account for the extreme optimization of the genetic code in nature. And, in fact, the relationships between coding assignments and amino acid biosynthesis appear to result from a statistical artifact, and nothing more.11 In other words, Wong’s ideas don’t work.

    That brings us back to the question of how to account for the genetic code’s optimization and design.

    As I see it, in the same way that two NBA superstars work together to help produce a championship-caliber team, the genetic code’s optimization and the failure of every evolutionary model to account for it form a potent one-two punch that makes a case for a Creator.

    And that is worth talking about.

    Resources

    Endnotes
    1. Steven E. Massey, “Searching of Code Space for an Error-Minimized Genetic Code via Codon Capture Leads to Failure, or Requires at Least 20 Improving Codon Reassignments via the Ambiguous Intermediate Mechanism,” Journal of Molecular Evolution 70, no. 1 (January 2010): 106–15, doi:10.1007/s00239-009-9313-7.
    2. F. H. C. Crick, “The Origin of the Genetic Code,” Journal of Molecular Biology 38, no. 3 (December 28, 1968): 367–79, doi:10.1016/0022-2836(68)90392-6.
    3. Hubert P. Yockey, Information Theory and Molecular Biology (Cambridge, UK: Cambridge University Press, 1992), 180–83.
    4. Stefan Wichmann and Zachary Ardern, “Optimality of the Standard Genetic Code Is Robust with Respect to Comparison Code Sets,” Biosystems 185 (November 2019): 104023, doi:10.1016/j.biosystems.2019.104023.
    5. Massey, “Searching of Code Space.”
    6. Massey, “Searching of Code Space.”
    7. Ramin Amirnovin, “An Analysis of the Metabolic Theory of the Origin of the Genetic Code,” Journal of Molecular Evolution 44, no. 5 (May 1997): 473–76, doi:10.1007//PL00006170.
  • New Insights into Genetic Code Optimization Signal Creator’s Handiwork

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Oct 16, 2019

    I knew my career as a baseball player would be short-lived when, as a thirteen-year-old, I made the transition from Little League to the Babe Ruth League, which uses official Major League Baseball rules. Suddenly there were a whole lot more rules for me to follow than I ever had to think about in Little League.

    Unlike in Little League, at the Babe Ruth level the hitter and base runners have to know what the other is going to do. Usually, the third-base coach is responsible for this communication. Before each pitch is thrown, the third-base coach uses a series of hand signs to relay instructions to the hitter and base runners.

    blog__inline--new-insights-into-genetic-code

    Credit: Shutterstock

    My inability to pick up the signs from the third-base coach was a harbinger for my doomed baseball career. I did okay when I was on base, but I struggled to pick up his signs when I was at bat.

    The issue wasn’t that there were too many signs for me to memorize. I struggled recognizing the indicator sign.

    To prevent the opposing team from stealing the signs, it is common for the third-base coach to use an indicator sign. Each time he relays instructions, the coach randomly runs through a series of signs. At some point in the sequence, the coach gives the indicator sign. When he does that, it means that the next signal is the actual sign.

    All of this activity was simply too much for me to process. When I was at the plate, I couldn’t consistently keep up with the third-base coach. It got so bad that a couple of times the third-base coach had to call time-out and have me walk up the third-base line, so he could whisper to me what I was to do when I was at the plate. It was a bit humiliating.

    Codes Come from Intelligent Agents

    The signs relayed by a third-base coach to the hitter and base runners are a type of codea set of rules used to convert and convey information across formats.

    Experience teaches us that it takes intelligent agents, such as baseball coaches, to devise codes, even those that are rather basic in their design. The more sophisticated a code, the greater the level of ingenuity required to develop it.

    Perhaps the most sophisticated codes of all are those that can detect errors during data transmission.

    I sure could have used a code like that when I played baseball. It would have helped me if the hand signals used by the third-base coach were designed in such a way that I could always understand what he wanted, even if I failed to properly pick up the indicator signal.

    The Genetic Code

    As it turns out, just such a code exists in nature. It is one of the most sophisticated codes known to us—far more sophisticated than the best codes designed by the brightest computer engineers in the world. In fact, this code resides at the heart of biochemical systems. It is the genetic code.

    This biochemical code consists of a set of rules that define the information stored in DNA. These rules specify the sequence of amino acids that the cell’s machinery uses to build proteins. In this process, information formatted as nucleotide sequences in DNA is converted into information formatted as amino acid sequences in proteins.

    Moreover, the genetic code is universal, meaning that all life on Earth uses it.1

    Biochemists marvel at the design of the genetic code, in part because its structure displays exquisite optimization. This optimization includes the capacity to dramatically curtail errors that result from mutations.

    Recently, a team from Germany identified another facet of the genetic code that is highly optimized, further highlighting its remarkable qualities.2

    The Optimal Genetic Code

    As I describe in The Cell’s Design, scientists from Princeton University and the University of Bath (UK) quantified the error-minimization capacity of the genetic code during the 1990s. Their work indicated that the universal genetic code is optimized to withstand the potentially harmful effects of substitution mutations better than virtually any other conceivable genetic code.3

    In 2018, another team of researchers from Germany demonstrated that the universal genetic code is also optimized to withstand the harmful effects of frameshift mutations—again, better than other conceivable codes.4

    In 2007, researchers from Israel showed that the genetic code is also optimized to harbor overlapping codes.5 This is important because, in addition to the genetic code, regions of DNA harbor other overlapping codes that direct the binding of histone proteins, transcription factors, and the machinery that splices genes after they have been transcribed.

    The Robust Optimality of the Genetic Code

    With these previous studies serving as a backdrop, the German research team wanted to probe more deeply into the genetic code’s optimality. These researchers focused on potential optimality of three properties of the genetic code: (1) resistance to harmful effects of substitution mutations, (2) resistance to harmful effects of frameshift mutations, and (3) capacity to support overlapping genes.

    As with earlier studies, the team assessed the optimality of the naturally occurring genetic code by comparing its performance with sets of random codes that are conceivable alternatives. For all three property comparisons, they discovered that the natural (or standard) genetic code (SGC) displays a high degree of optimality. The researchers write, “We find that the SGC’s optimality is very robust, as no code set with no optimised properties is found. We therefore conclude that the optimality of the SGC is a robust feature across all evolutionary hypotheses.”6

    On top of this insight, the research team adds one other dimension to multidimensional optimality of the genetic code: its capacity to support overlapping genes.

    Interestingly, the researchers also note that the results of their work raise significant challenges to evolutionary explanations for the genetic code, pointing to the code’s multidimensional optimality that is extreme in all dimensions. They write:

    We conclude that the optimality of the SGC is a robust feature and cannot be explained by any simple evolutionary hypothesis proposed so far. . . . the probability of finding the standard genetic code by chance is very low. Selection is not an omnipotent force, so this raises the question of whether a selection process could have found the SGC in the case of extreme code optimalities.7

    While natural selection isn’t omnipotent, a transcendent Creator would be, and could account for the genetic code’s extreme optimality.

    The Genetic Code and the Case for a Creator

    In The Cell’s Design, I point out that our common experience teaches us that codes come from minds. It’s true on the baseball diamond and true in the computer lab. By analogy, the mere existence of the genetic code suggests that biochemical systems come from a Mind—a conclusion that gains additional support when we consider the code’s sophistication and exquisite optimization.

    The genetic code’s ability to withstand errors that arise from substitution and frameshift mutations, along with its optimal capacity to harbor multiple overlapping codes and overlapping genes, seems to defy naturalistic explanation.

    As a neophyte playing baseball, I could barely manage the simple code the third-base coach used. How mind-boggling it is for me when I think of the vastly superior ingenuity and sophistication of the universal genetic code.

    And, just like the hitter and base runner work together to produce runs in baseball, the elegant design of the genetic code and the inability of evolutionary processes to account for its extreme multidimensional optimization combine to make the case that a Creator played a role in the origin and design of biochemical systems.

    With respect to the case for a Creator, the insight from the German research team hits it out of the park.

    Resources:

    Endnotes
    1. Some organisms have a genetic code that deviates from the universal code in one or two of the coding assignments. Presumably, these deviant codes originate when the universal genetic code evolves, altering coding assignments.
    2. Stefan Wichmann and Zachery Ardern, “Optimality of the Standard Genetic Code Is Robust with Respect to Comparison Code Sets,” Biosystems 185 (November 2019): 104023, doi:10.1016/j.biosystems.2019.104023.
    3. David Haig and Laurence D. Hurst, “A Quantitative Measure of Error Minimization in the Genetic Code,” Journal of Molecular Evolution 33, no. 5 (November 1991): 412–17, doi:1007/BF02103132; Gretchen Vogel, “Tracking the History of the Genetic Code,” Science 281, no. 5375 (July 17, 1998): 329–31, doi:1126/science.281.5375.329; Stephen J. Freeland and Laurence D. Hurst, “The Genetic Code Is One in a Million,” Journal of Molecular Evolution 47, no. 3 (September 1998): 238–48, doi:10.1007/PL00006381; Stephen J. Freeland et al., “Early Fixation of an Optimal Genetic Code,” Molecular Biology and Evolution 17, no. 4 (April 2000): 511–18, 10.1093/oxfordjournals.molbev.a026331.
    4. Regine Geyer and Amir Madany Mamlouk, “On the Efficiency of the Genetic Code after Frameshift Mutations,” PeerJ 6 (May 21, 2018): e4825, doi:10.7717/peerj.4825.
    5. Shalev Itzkovitz and Uri Alon, “The Genetic Code Is Nearly Optimal for Allowing Additional Information within Protein-Coding Sequences,” Genome Research 17, no. 4 (April 2007): 405–12, doi:10.1101/gr.5987307.
    6. Wichmann and Ardern, “Optimality.”
    7. Wichmann and Ardern, “Optimality.”
  • Is the Optimal Set of Protein Amino Acids Purposed by a Mind?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Oct 09, 2019

    As a graduate student and a postdoc, I spent countless hours in the lab doing research. Part of my work involved performing biochemical assays—laboratory procedures designed to measure the activities of biomolecules and biochemical systems.

    To get our assays to work properly, we had to carefully design and optimize each test before executing it with exacting precision in the laboratory. Optimizing these assays was no easy feat. It could take weeks of painstaking effort to get the protocols just right.

    My experiences working in the lab taught me some important lessons that I carry with me today as a Christian apologist. One of these lessons has to do with optimization. Optimized systems don’t just happen, whether they are laboratory procedures, manufacturing operations, or well-designed objects or devices. Instead, optimization results from the insights and efforts of intelligent agents, and therefore serves as a sure indicator of intelligent design.

    As it turns out, nearly every biochemical system appears to be highly optimized. For me, this fact indicates that life stems from a Mind. And as life scientists continue to characterize biochemical systems, they keep discovering more and more examples of biochemical optimization, as recent work by a large team of collaborators working at the Earth-Life Science Institute (ELSI) in Tokyo, Japan, illustrates.1

    These researchers uncovered more evidence that the twenty amino acids encoded by the genetic code possess the optimal set of physicochemical properties. If not for these properties, it would not be possible for the cell to build proteins that could support the wide range of activities required to sustain living systems. This insight gives us important perspective into the structure-function relationships of proteins. It also has theological significance, adding to the biochemical case for a Creator.

    Before describing the ELSI team’s work and its theological implications, a little background might be helpful for some readers. For those who are familiar with basic biochemistry, just skip ahead to Why These Twenty Amino Acids?

    Background: Protein Structure

    Proteins are large, complex molecules that play a key role in virtually all of the cell’s operations. Biochemists have long known that the three-dimensional structure of a protein dictates its function. Because proteins are such large, complex molecules, biochemists categorize protein structure into four different levels: primary, secondary, tertiary, and quaternary structures.

    blog__inline--is-the-optimal-set-of-protein-amino-acids-1

    Figure 1: The Four Levels of Protein Structure. Image credit: Shutterstock

    • A protein’s primary structure is the linear sequence of amino acids that make up each of its polypeptide chains.
    • The secondary structure refers to short-range three-dimensional arrangements of the polypeptide chain’s backbone arising from the interactions between chemical groups that make up its backbone. Three of the most common secondary structures are the random coil, alpha (α) helix, and beta (β) pleated sheet.
    • Tertiary structure describes the overall shape of the entire polypeptide chain and the location of each of its atoms in three-dimensional space. The structure and spatial orientation of the chemical groups that extend from the protein backbone are also part of the tertiary structure.
    • Quaternary structure arises when several individual polypeptide chains interact to form a functional protein complex.

    Background: Amino Acids

    The building blocks of proteins are amino acids. These compounds are characterized by having both an amino group and a carboxylic acid bound to a central carbon atom. Also bound to this carbon are a hydrogen atom and a substituent that biochemists call an R group.

    blog__inline--is-the-optimal-set-of-protein-amino-acids-2

    Figure 2: The Structure of a Typical Amino Acid. Image credit: Shutterstock

    The R group determines the amino acid’s identity. For example, if the R group is hydrogen, the amino acid is called glycine. If the R group is a methyl group, the amino acid is called alanine.

    Close to 150 amino acids are found in proteins. But only 19 amino acids (plus 1 imino acid, called proline) are specified by the genetic code. Biochemists refer to these 20 as the canonical set.

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    Figure 3: The Protein-Forming Amino Acids. Image credit: Shutterstock

    A protein’s primary structure forms when amino acids react with each other to form a linear chain, with the amino group of one amino acid combining with the carboxylic acid of another to form an amide linkage. (Sometimes biochemists call the linkage a peptide bond.)

    blog__inline--is-the-optimal-set-of-protein-amino-acids-4

    Figure 4: The Chemical Linkage between Amino Acids. Image credit: Shutterstock

    The repeating amide linkages along the amino acid chain form the protein’s backbone. The amino acids’ R groups extend from the backbone, creating a distinct physicochemical profile along the protein chain for each unique amino acid sequence. To first approximation, this unique physicochemical profile dictates the protein’s higher-order structures and, hence, the protein’s function.

    Why These Twenty Amino Acids?

    Research has revealed that the set of amino acids used to build proteins is universal. In other words, the proteins found in every organism on Earth are made up of the same canonical set.

    Biochemists have long wondered: Why these 20 amino acids?

    In the early 1980s biochemists discovered that an exquisite molecular rationale undergirds the amino acid set used to make proteins.2 Every aspect of amino acid structure has to be precisely the way it is for life to be possible. On top of that, biochemists concluded that the set of 20 amino acids possesses the “just-right” physical and chemical properties that evenly and uniformly vary across a broad range of size, charge, and hydrophobicity (water resistance). In fact, it appears as if the amino acids selected for proteins seem to form a uniquely optimal set of 20 amino acids compared to random sets of amino acids.3

    With these previous studies as a backdrop, the ELSI investigators wanted to develop a better understanding of the optimal nature of the universal set of amino acids used to build proteins. They also wanted to gain insight into the origin of the canonical set.

    To do this they used a library of 1,913 amino acids (including the 20 amino acids that make up the canonical set) to construct random sets of amino acids. The researchers varied the set sizes from 3 to 20 amino acids and evaluated the performance of the random sets in terms of their capacity to support: (1) the folding of protein chains into three-dimensional structures; (2) protein catalytic activity; and (3) protein solubility.

    They discovered that if a random set of amino acids included even a single amino acid from the canonical set, it dramatically out-performed random sets of the same size without any of the canonical amino acids. Based on these results, the researchers concluded that each of the 20 amino acids used to build proteins stands out, possessing highly unusual properties that make them ideally suited for their biochemical role, confirming the results of previous studies.

    An Evolutionary Origin for the Canonical Set?

    The ELSI researchers believe that—from an evolutionary standpoint—these results also shed light as to how the canonical set of amino acids emerged. Because of the unique adaptive properties of the canonical amino acids, the researchers speculate that “each time a CAA [canonical amino acid] was discovered and embedded during evolution, it provided an adaptive value unusual among many alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs.”4

    In other words, the researchers offer the conjecture that whenever the evolutionary process stumbled upon one of the amino acids in the canonical set and incorporated it into nascent biochemical systems, the addition offered such a significant evolutionary advantage that it became instantiated into the biochemistry of the emerging cellular systems. Presumably, as this selection process occurred repeatedly over time, members of the canonical set would be added, one by one, to the evolving amino acid set, eventually culminating in the full canonical set.

    Scientists find further support for this scenario in the following observation: some of the canonical amino acids seemingly play a more important role in optimizing smaller sets of amino acids, some play a more important role in optimizing intermediate size sets of amino acids, and others play a more prominent role in optimizing larger sets. They argue that this difference may reflect the sequence by which amino acids were added to the evolving set of amino acids as life emerged.

    On the surface, this evolutionary explanation is not unreasonable. But more careful consideration of the idea raises concerns. For example, just because a canonical amino acid becomes incorporated into a set of amino acids and improves its adaptive value doesn’t mean that the resulting set of amino acids could produce the range of proteins with the solubility, foldability, and catalytic range needed to support life processes. Intuitively, it seems to me as a biochemist, that there must be a threshold for the number of canonical amino acids in any set of amino acids for it to have the range of physicochemical properties needed to build all the proteins needed to support minimal life.

    I also question this evolutionary scenario because some of the amino acids that optimize smaller sets would not have been the ones present initially on the early Earth because they cannot be made by prebiotic reactions. Instead, many of the amino acids that optimize smaller sets can only be generated through biosynthetic routes that must have emerged much later in any evolutionary scenario for the origin of life.5 This limitation also means that the only way for some of the canonical amino acids to become incorporated into the canonical set is that multi-step biosynthetic routes for those amino acids evolved first. But if the full canonical set isn’t available, then it is questionable if the proteins needed to catalyze the biosynthesis of these amino acid would exist, resulting in a chicken-and-egg dilemma.

    In light of these concerns, is there a better explanation for the highly optimized canonical set of amino acids?

    A Creator’s Role?

    Optimality of the universal set of protein amino acids finds explanation if life stems from a Creator’s handiwork. As noted, optimization is an indicator of intelligent design, achieved through foresight and preplanning. Optimization requires inordinate attention to detail and careful craftsmanship. By analogy, the optimized biochemistry epitomized by the amino acid set that makes up proteins rationally points to the work of a Creator.

    Is There a Biochemical Anthropic Principle?

    This discovery also leads to another philosophical implication: It lends support to the existence of a biochemical anthropic principle.

    The ELSI researchers speculate that no matter the starting point in the evolutionary process, the pathways will all converge at the canonical set of amino acids because of the acids’ unusual adaptive properties. In other words, the amino acids that make up the universal set of protein-coding amino acids are not the outworking of an historically contingent evolutionary process, but instead seem to be fundamentally prescribed by the laws of nature. To put it differently, it appears as if the canonical set of amino acids has been preordained in some way.6 One of the study’s authors, Rudrarup Bose, suggests that “Life may not be just a set of accidental events. Rather, there may be some universal laws governing the evolution of life.”7

    Though I prefer to see the origin of life as a creation event, it is important to recognize that even if one were to adopt an evolutionary perspective on life’s origin, it looks as if a Mind is responsible for jimmy-rigging the process to a predetermined endpoint. It looks as if a Mind purposed for life to be present in the universe and structured the laws of nature so that, in this case, the uniquely optimal canonical set of amino acids would inevitably emerge.

    Along these lines, it is remarkable to think that the canonical set of amino acids has the precise properties needed for life to exist. This “coincidence” is eerie, to say the least. As a biochemist, I interpret this coincidence as evidence that our universe has been designed for a purpose. It is provocative to think that regardless of one’s perspective on the origin of life, the evidence converges toward a single conclusion: namely that life manifests from an intelligent agent—God.

    Resources

    The Optimality of Biochemical Systems

    The Biochemical Anthropic Principle

    Endnotes
    1. Melissa Ilardo et al., “Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subset,” Scientific Reports 9, no. 12468 (August 28, 2019), doi:10.1038/s41598-019-47574-x.
    2. Arthur L. Weber and Stanley L. Miller, “Reasons for the Occurrence of the Twenty Coded Protein Amino Acids,” Journal of Molecular Evolution 17, no. 5 (September 1981): 273–84, doi:10.1007/BF01795749; H. James Cleaves II, “The Origin of the Biologically Coded Amino Acids,” Journal of Theoretical Biology 263, no. 4 (April 2010): 490–98, doi:10.1016/j.jtbi.2009.12.014.
    3. Gayle K. Philip and Stephen J. Freeland, “Did Evolution Select a Nonrandom ‘Alphabet’ of Amino Acids?” Astrobiology 11, no. 3 (April 2011), 235–40, doi:10.1089/ast.2010.0567; Matthias Granhold et al., “Modern Diversification of the Amino Acid Repertoire Driven by Oxygen,” Proceedings of the National Academy of Sciences, USA 115, no. 1 (January 2, 2018): 41–46, doi:10.1073/pnas.1717100115.
    4. Ilardo et al., “Adaptive Properties.”
    5. J. Tze-Fei Wong and Patricia M. Bronskill, “Inadequacy of Prebiotic Synthesis as Origin of Proteinous Amino Acids,” Journal of Molecular Evolution 13, no. 2 (June 1979): 115–25, doi:10.1007/BF01732867.
    6. Tokyo Institute of Technology, “Scientists Find Biology’s Optimal ‘Molecular Alphabet’ May Be Preordained,” ScienceDaily, September 10, 2019, http://www.sciencedaily.com/releases/2019/09/190910080017.htm.
    7. Tokyo Institute, “Scientists Find.”
  • Can Dinosaurs Be Resurrected from Extinction?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Sep 25, 2019

    If you could visit a theme park that offered you a chance to view and even interact with real-life dinosaurs, would you go? I think I might. Who wants to swim with dolphins when you can hang out with dinosaurs? Maybe even ride one?

    Well, if legendary paleontologist Jack Horner has his way, we just might get our wish—and, it could be much sooner than any of us realize. Horner is a champion of the scientific proposal to resurrect dinosaurs from extinction. And it looks like this idea might have a real chance at success.

    Horner’s not taking the “Jurassic Park/World” approach of trying to clone dinosaurs from ancient DNA (which won’t work for myriad technical reasons). He wants to transform birds into dinosaur-like creatures by experimentally manipulating their developmental processes in a laboratory setting.

    The Evolutionary Connection between Birds and Dinosaurs

    The basis for Horner’s idea rises out of the evolutionary paradigm. Most paleontologists think that birds and dinosaurs share an evolutionary history. These scientists argue that shared anatomical features (a key phrase we’ll return to) between birds and certain dinosaur taxa demonstrate their evolutionary connection. Currently, paleontologists place dinosaurs into two major groups: avian and nonavian dinosaurs. Accordingly, paleontologists think that birds are the evolutionary descendants of dinosaurs.

    So, if Horner and others are successful, what does this mean for creation? For evolution?

    Reverse Evolution

    In effect, Horner and other interested scientists seek to reverse what they view as the evolutionary process, converting birds into an evolutionarily ancestral state. Dubbed reverse evolution, this approach will likely become an important facet of paleontology in the future. Evolutionary biologists believe that they can gain understanding of how biological transformations took place during life’s history by experimentally reverting organisms to their ancestral state. Reverse evolution experiments fuse insights from paleontology with those from developmental biology, molecular biology, comparative embryology, and genomics. Many life scientists are excited, because, for the first time, researchers can address questions in evolutionary biology using an experimental strategy.

    Proof-of-Principle Studies

    The first bird that researchers hope to reverse-evolve into a dinosaur-like creature is the chicken (Gallus gallus). This makes sense. We know a whole lot about chicken biology, and life scientists can leverage this understanding to precisely manipulate the embryonic progression of chicks so that they develop into dinosaur-like creatures.

    As I described previously (see Resources for Further Exploration), in 2015 researchers from Harvard and Yale Universities moved the scientific community one step closer to creating a “chickenosaurus” by manipulating chickens in ovo to develop snout-like structures, instead of beaks, just like dinosaurs.1

    Now, two additional proof-of-principle studies demonstrate the feasibility of creating a chickenosaurus. Both studies were carried out by a research team from the Universidad de Chile.

    In one study, the research team coaxed chicken embryos to develop a dinosaur-like foot structure, instead of the foot structure characteristic of birds.2 A bird’s foot has a perching digit that points in the backward direction, in opposition to the other toes. The perching digit allows birds to grasp. In contrast, the corresponding toe in dinosaurs is nonopposable, pointing forward.

    blog__inline--can-dinosaurs-be-resurrected-from-extinction-1

    Figure 1: Dinosaur Foot Structure. Image credit: Shutterstock

    blog__inline--can-dinosaurs-be-resurrected-from-extinction-2

    Figure 2: Bird Foot Structure. Image credit: Shutterstock

    The researchers took advantage of the fact that vertebrate skeletons are plastic, meaning that their structure can be altered by muscle activity. These types of skeletal alterations most commonly occur during embryonic and juvenile stages of growth and development.

    Investigators discovered that muscle activity causes the perching toe of birds to reorient during embryonic development from originally pointing forward to adopting an opposable orientation. Specifically, the activity of three muscles (flexor hallucis longus, flexor hallucis brevis, and musculus extensor hallucis longus) creates torsion that twists the first metatarsal, forcing the perching digit into the opposable position.

    The team demonstrated that by injecting the compound decamethonium bromide into a small opening in the eggshell just before the torsional twisting of the first metatarsal takes place, they could prevent this foot bone from twisting. The compound causes muscle paralysis, which limits the activity of the muscles that cause the torsional stress on the first metatarsal. The net result: the chick developed a dinosaur-like foot structure.

    In a second study, this same research team was able to manipulate embryonic development of chicken embryos to form a dinosaur-like leg structure.3 The lower legs of vertebrates consist of two bones: the tibia and the fibula. In most vertebrates, the fibula is shaped like a tube, extending all the way to the ankle. In birds, the fibula is shorter than the tibia and has a spine-like morphology (think chicken drumsticks).

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    Figure 3: The Lower Leg of a Chicken. Image credit: Shutterstock

    Universidad de Chile researchers discovered that the gene encoding the Indian Hedgehog protein becomes active at the distal end of the fibula during embryonic development of the lower leg in chicks, causing the growth of the fibula to cease. They also learned that the event triggering the increased activity of the Indian Hedgehog gene likely relates to the depletion of the Parathyroid Hormone-Related Protein near the distal end of the fibula. This protein plays a role in stimulating bone growth.

    The researchers leveraged this insight to experimentally create a chick with dinosaur-like lower legs. Specifically, they injected the amniotic region of the chicken embryo with cyclopamine. This compound inhibits the activity of Indian Hedgehog. They discovered that this injection altered fibula development so that it was the same length as the tibia, contacting the ankle, just like in dinosaurs.

    These two recent experiments on foot structure along with the previous one on snout structure represent science at its best. While the experiments reside at the proof-of-principle stage, they still give scientists like Jack Horner reason to think that we just might be able to resurrect dinosaurs from extinction one day. These experiments also raise scientific and theological questions.

    Do Studies in Reverse Evolution Support the Evolutionary Paradigm?

    On the surface, these studies seemingly make an open-and-shut case for the evolutionary origin of birds. It is impressive that researchers can rewind the tape of life and convert chickens into dinosaur-like creatures.

    But deeper reflection points in a different direction.

    All three studies highlight the amount of knowledge and insight about the developmental process required to carry out the reverse evolution experiments. The ingenious strategy the researchers employed to alter the developmental trajectory is equally impressive. They had to precisely time the addition of chemical agents at the just-right levels in order to influence muscle activity in the embryo’s foot or gene activity in the chick’s developing lower legs. Recognizing the knowledge, ingenuity, and skill required to alter embryological development in a coherent way that results in a new type of creature forces the question: Is it really reasonable to think that unguided, historically contingent processes could carry out such transformations when small changes in development can have profound effects on an organism’s anatomy?

    It seems that the best the evolutionary process could achieve would be the generation of “monsters” with little hope of survival. Why? Because evolutionary mechanisms can only change gene expression patterns in a random, haphazard manner. I would contend that the coherent, precisely coordinated genetic changes needed to generate one biological system from another signals a Creator’s handiwork, not undirected evolutionary mechanisms, as the explanation for life’s history.

    Can a Creation Model Approach Explain the Embryological Similarities?

    Though the work in reverse evolution seems to fit seamlessly within an evolutionary framework, observations from these studies can be explained from a creation model perspective.

    Key to this explanation is the work of Sir Richard Owen, a preeminent biologist who preceded Charles Darwin. In contemporary biology, scientists view shared features possessed by related organisms as evidence of common ancestry. Birds and theropod dinosaurs would be a case in point. But for Owen, shared anatomical features reflected an archetypal design that originated in the Mind of the First Cause. Toward this end, the anatomical features shared by birds and theropods can be understood as reflecting common design, not common descent.

    Though few biologists embrace Owen’s ideas today, it is important to note that his ideas were not tried and found wanting. They simply were abandoned in favor of Darwin’s theory, which many biologists preferred because it provided a mechanistic explanation for life’s history and the origin of biological systems. In fact, Darwin owes a debt of gratitude to Owen’s thinking. Darwin coopted the idea of the archetype, but then replaced the canonical blueprint that existed in the Creator’s Mind (per Owen) with a hypothetical common ancestor.

    This archetypal approach to biology can account for the results of reverse-evolution studies. Accordingly, the researchers have discovered differences in the developmental program that affect variations in the archetype, yielding differences in modern birds and long-extinct dinosaurs.

    The idea of the archetype can extend to embryonic growth and development. One could argue that the Creator appears to have developed a core (or archetypal) developmental algorithm that can be modified to yield disparate body plans. From a creation model standpoint, then, the researchers from Harvard and Yale Universities and the Universidad de Chile didn’t reverse the evolutionary process. They unwittingly reverse-engineered a dinosaur-like developmental algorithm from a bird-like developmental program.

    Why Would God Create Using the Same Design Templates?

    There may well be several reasons why a Creator would design living systems around a common set of templates. In my estimation, the most significant reason is discoverability.

    Shared anatomical and physiological features, as well as shared features of embryological development make it possible to apply what we learn by studying one organism to others. This shared developmental program makes it possible to use our understanding of embryological growth and development to reengineer a bird into a dinosaur-like creature. Discoverability makes it easier to appreciate God’s glory and grandeur, as evinced in biochemical systems by their elegance, sophistication, and ingenuity.

    Discoverability also reflects God’s providence and care for humanity. If not for the shared features, it would be nearly impossible for us to learn enough about the living realm for our benefit. Where would biomedical science be without the ability to learn fundamental aspects about our biology by studying model organisms such as chickens? And where would our efforts to re-create dinosaurs be if not for the biological designs they share with birds?

    Resources for Further Exploration

    Reverse Evolution

    Shared Biological Designs and the Creation Model

    Endnotes
    1. Bhart-Anjan S. Bhullar et al., “A Molecular Mechanism for the Origin of a Key Evolutionary Innovation, the Bird Beak and Palate, Revealed by an Integrative Approach to Major Transitions in Vertebrate History,” Evolution 69, no. 7 (2015): 1665–77, doi:10.1111/evo.12684.
    2. João Francisco Botelho et al., “Skeletal Plasticity in Response to Embryonic Muscular Activity Underlies the Development and Evolution of the Perching Digit of Birds,” Scientific Reports 5 (May 14, 2015): 9840, doi:10.1038/srep09840.
    3. João Francisco Botelho et al., “Molecular Developments of Fibular Reduction in Birds and Its Evolution from Dinosaurs,” Evolution 70, no. 3 (March, 2016): 543–54, doi:10.1111/evo.12882.
  • Primate Thanatology and the Case for Human Exceptionalism

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Sep 18, 2019

    I will deliver this people from the power of the grave;
    I will redeem them from death.
    Where, O death, are your plagues?
    Where, O grave, is your destruction?

    Hosea 13:14

    It was the first time someone I knew died. I was in seventh grade. My classmate’s younger brother and two younger sisters perished in a fire that burned his family’s home to the ground. We lived in a small rural town in West Virginia at the time. Everyone knew each other and the impact of that tragedy reverberated throughout the community.

    I was asked to be a pallbearer at the funeral. To this day, I remember watching my friend’s father with a cast on one arm and another on one of his legs, hobble up to each of the little caskets to touch them one last time as he sobbed uncontrollably right before we lifted and carried the caskets to the waiting hearses.

    Death is part of life and our reaction to death is part of what makes us human. But, are humans unique in this regard?

    Funerary Practices

    Human responses to death include funerary practices—ceremonies that play an integral role in the final disposition of the body of the deceased.

    Anthropologists who study human cultures see funerals as providing important scientific insight into human nature. These scientists define funerals as cultural rituals designed to honor, remember, and celebrate the life of those who have died. Funerals provide an opportunity for people to express grief, mourn loss, offer sympathy, and support the bereaved. Also, funerals often serve a religious purpose that includes (depending on the faith tradition) praying for the person who has died, helping his or her soul transition to the afterlife (or reincarnate).

    Funerary Practices and Human Exceptionalism

    For many anthropologists, human funerary practices are an expression of our capacities for:

    • symbolism
    • open-ended generative manipulation of symbols
    • theory of mind
    • complex, hierarchical social interactions

    Though the idea of human exceptionalism is controversial within anthropology today, a growing minority of anthropologists argue that the combination of these qualities sets us apart from other creatures. They make us unique and exceptional.

    As a Christian, I view this set of qualities as scientific descriptors of the image of God. That being the case, then, from my vantage point, human funerary practices (along with language, music, and art) are part of the body of evidence that we can marshal to make the case that human beings uniquely bear God’s image.

    What about Neanderthals?

    But are human beings really unique and exceptional?

    Didn’t Neanderthals bury their dead? Didn’t these hominins engage in funerary practices just like modern humans do?

    If the answer to these questions is yes, then for some people it undermines the case for human uniqueness and exceptionalism and, along with it, the scientific case for the image of God. If Neanderthal funerary practices flow out of the capacity for symbolism, open-ended generative capacity, etc., then it means that Neanderthals must have been like us. They must have been exceptional, too, and humans don’t stand apart from all other creatures on Earth, as the Scriptures teach.

    Did Neanderthals Bury Their Dead?

    But, could these notions about Neanderthal exceptionalism be premature? Although there is widespread belief that Neanderthals buried their dead in a ritualistic manner and even though this claim can be attested in the scientific literature, a growing body of archeological evidence challenges this view.

    Many anthropologists question if Neanderthal burials were in fact ritualistic. (If they weren’t, then it most likely indicates that these hominins didn’t have a concept of the afterlife—a concept that requires symbolism and open-ended generative capacities.) Others go so far as to question if Neanderthals buried their dead at all. (For an in-depth discussion of the scientific challenges to Neanderthal burials, see the Resources section below.)

    Were Neanderthal Burials an Evolutionary Precursor to Human Funerary Practices?

    It is not unreasonable to think that these hominins may well have disposed of corpses and displayed some type of response when members of their group died. Over the centuries, keen observers (including primatologists, most recently) have documented nonhuman primates inspecting, protecting, retrieving, carrying, and dragging the dead bodies of members of their groups.1 In light of these observations, it makes sense to think that Neanderthals may have done something similar.

    While it doesn’t appear that Neanderthals responded to death in the same way we do, it is tempting (within the context of the evolutionary paradigm) to view Neanderthal behavior as an evolutionary stepping-stone to the funerary practices of modern humans.

    But, is this transitional view the best explanation for Neanderthal burials—assuming that these hominins did, indeed, dispose of group members’ corpses? Research in thanatology (the study of dying and death) among nonhuman primates holds the potential to shed light on this question.

    The Nonhuman Primate Response to Death

    Behavioral evolution researchers André Gonçalves and Susana Caravalho recently reviewed studies in primate thanatology—categorizing and interpreting the way these creatures respond to death. In the process, they sought to explain the role the death response plays among various primate groups.

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    Figure 1: Monkey Sitting over the Body of a Deceased Relative. Image credit: Shutterstock

    When characterizing the death response of nonhuman primates, Gonçalves and Caravalho group the behaviors of these creatures into two categories: (1) responses to infant deaths and (2) responses to adult deaths.

    In most primate taxa (classified groups), when an infant dies the mother will carry the dead baby for days before abandoning it, often grooming the corpse and swatting away flies. Eventually, she will abandon it. Depending on the taxon, in some instances young females will carry the infant’s remains for a few days after the mother abandons it. Most other members in the group ignore the corpse. At times, they will actively avoid both mother and corpse when the stench becomes overwhelming.

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    Figure 2: Baboon Mother with a Child. Image credit: Shutterstock

    The death of an adult member of the group tends to elicit a much more pervasive response than does the death of an infant. The specific nature of the response depends upon the taxon and also on other factors such as: (1) the bond between individual members of the group and the deceased; (2) the social status of the deceased; and (3) the group structure of the particular taxon. Typically, the closer the bond between the deceased and the group member the longer the duration of the death response. The same is true if the deceased is a high-ranking member of the group.

    Often the death response includes vocalizations that connote alarm and distress. Depending on the taxon, survivors may hit and pull at the corpse, as if trying to rouse it. Other times, it appears that survivors hit the corpse out of frustration. Sometimes groups members will sniff at the corpse or peer at it. In some taxa, survivors will groom the corpse or stroke it gently, while swatting away flies. In other taxa, survivors will stand vigil over the corpse, guarding it from scavengers.

    In some instances, survivors return to the corpse and visit it for days. After the corpse is disposed, group members may continue to visit the site for quite some time. In other taxa, group members may avoid the death site. Both behaviors indicate that group members understand that an event of great importance to the group took place at the site where a member died.

    Are Humans and Nonhuman Primates Different in Degree? Or Kind?

    It is clear that nonhuman primates have an awareness of death and, for some primate taxa, it seems as if members of the group experience grief. Some anthropologists and primatologists see this behavior as humanlike. It’s easy to see why. We are moved by the anguish and confusion these creatures seem to experience when one of their group members dies.

    For the most part, these scientists would agree that the human response to death is more complex and sophisticated. Yet, they see human behavior as differing only in degree rather than kind when compared to other primates. Accordingly, they interpret primate death awareness as an evolutionary antecedent to the sophisticated funerary practices of modern humans, with Neanderthal behavior part of the trajectory. And for this reason, they maintain that human beings really aren’t unique or exceptional.

    The Trouble with Anthropomorphism

    One problem with this conclusion (even within an evolutionary framework) is that it fails to account for the human tendency toward anthropomorphism. As part of our human nature, we possess theory of mind. We recognize that other human beings have minds like ours. And because of this capability, we know what other people are thinking and feeling. But, we don’t know how to turn this feature on and off. As a result, we also apply theory of mind to animals and inanimate objects, attributing humanlike behaviors and motivations to them, though they don’t actually possess these qualities.

    British ethnologist Marian Stamp Dawkins argues in her book Why Animals Matter that scientists studying animal behavior fall victim to the tendency to anthropomorphize just as easily as the rest of us. Too often, researchers interpret experimental results from animal behavioral studies and from observations of animal behavior in captivity and the wild in terms of human behavior. When they do, these researchers ascribe human mental experiences—thoughts and feelings—to animals. Dawkins points out that when investigators operate this way, it leads to untestable hypotheses because we can never truly know what occurs in animal minds. Moreover, Dawkins argues that we tend to prefer anthropomorphic interpretations to other explanations. She states, “Anthropomorphism tends to make people go for the most human-like explanation and ignore the other less exciting ones.”2

    A lack of awareness of our tendency toward anthropomorphism raises questions about the all-too-common view that the death response of nonhuman primates—and Neanderthals—is humanlike and an evolutionary antecedent to modern human funerary practices. This is especially true in light of the explanation offered by Gonçalves and Caravalho for the death response in primates.

    The two investigators argue that the response of mothers to the death of their infants is actually maladaptive (from an evolutionary perspective). Carrying around dead infants and caring for them is energetically costly and hinders their locomotion. Both consequences render them vulnerable to predators. The pair explain this behavior by arguing that the mother’s response to the death of her infant falls on the continuum of care-taking behavior and can be seen as a trade-off. In other words, nonhuman primate mothers who have a strong instinct to care for their offspring will ensure the survival of their infant. But if the infant dies, the instinct is so strong that they will continue to care for it after its death.

    Gonçalves and Caravalho also point out that the death response toward adult members of the group plays a role in reestablishing new group dynamics. Depending on the primate taxon, the death of members shifts the group’s hierarchical structure. This being the case, it seems reasonable to think that the death response helps group members adjust to the new group structure as survivors take on new positions in the hierarchy.

    Finally, as Dawkins argues, we can’t know what takes place in the minds of animals. Therefore, we can’t legitimately attribute human mental experiences to animals. So, while it may seem to us as if some nonhuman primates experience grief as part of the death response, how do we know that this is actually the case? Evidence for grief often consists of loss of appetite and increased vocalizations. However, though these changes occur in response to the death of a group member, there may be other explanations for these behaviors that have nothing to do with grief at all.

    Death Response in Nonhuman Primates and Neanderthals

    Study of primate thanatology also helps us to put Neanderthal burial practices (assuming that these hominins buried dead group members) into context. Often, when anthropologists interpret Neanderthal burials (from an evolutionary perspective), they are comparing these practices to human funerary practices. This comparison makes it seem like Neanderthal burials are part of an evolutionary trajectory toward modern human behavior and capabilities.

    But what if the death response of nonhuman primates is factored into the comparison? When we add a second endpoint, we find that the Neanderthal response to death clusters more closely to the responses displayed by nonhuman primates than to modern humans. And as remarkable as the death response of nonhuman primates may be, it is categorically different from modern human funerary practices. To put it another way, modern human funerary practices reflect our capacity for symbolism, open-ended manipulation of symbols, theory of mind, etc. In contrast, the death response of nonhuman primates and hominins, such as Neanderthals, seems to serve utilitarian purposes. So, it isn’t the presence or absence of the death response that determines our exceptional nature. Instead, it is a death response shaped by our capacity for symbolism and open-ended generative capacity that highlights our exceptional uniqueness.

    Modern humans really do seem to stand apart compared to all other creatures in a way that aligns with the biblical claim that human beings uniquely possess and express the image of God.

    RTB’s biblical creation model for human origins, described in Who Was Adam?, views hominins such as Neanderthals as creatures created by God’s divine fiat that possess intelligence and emotional capacity. These animals were able to employ crude tools and even adopt some level of “culture,” much like baboons, gorillas, and chimpanzees. But they were not spiritual beings made in God’s image. That position—and all of the intellectual, relational, and symbolic capabilities that come with it—remains reserved for modern humans alone.

    Resources for Further Exploration

    Did Neanderthals Bury Their Dead?

    Nonhuman Primate Behavior

    Problem-Solving in Animals and Human Exceptionalism

    Endnotes
    1. André Gonçalves and Susana Caravalho, “Death among Primates: A Critical Review of Nonhuman Primate Interactions towards Their Dead and Dying,” Biological Reviews 94, no. 4 (April 4, 2019), doi:10.1111/brv.12512.
    2. Marian Stamp Dawkins, Why Animals Matter: Animal Consciousness, Animal Welfare, and Human Well-Being (New York, Oxford University Press, 2012), 30.
  • Simple Biological Rules Affirm Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Sep 04, 2019

    “Biology is the study of complicated things that give the appearance of having been designed for a purpose.”
    –Richard Dawkins

    To say that biological systems are complicated is an understatement.

    When I was in college, I had some friends who avoided taking courses in the life sciences because of the complexity of biological systems. On the other hand, I found the complexity alluring. It’s what drew me to biochemistry. I love to immerse myself in the seemingly never-ending intricacies of biomolecular systems and try to make sense of them.

    Perhaps nothing exemplifies the daunting complexity of biochemistry more than intermediary metabolism.

    Order in the Midst of Biochemical Complexity

    I remember a conversation I had years ago with a first-year graduate student who worked in the same lab as me when I was a postdoc at the University of Virginia. He was complaining about all the memorization he had to do for the course he was taking on intermediary metabolism. How else was he going to become conversant with all the different metabolic routes in the cell?

    I told him that he was approaching his classwork in the wrong way. Despite the complexity and chemical diversity of the metabolic pathways in the cell, a set of principles exists that dictates the architecture and operation of metabolic routes. I encouraged my lab mate to learn these principles because, once he did, he would be able to use them to write out all of the metabolic routes with minimal memorization.

    These principles make sense of the complexity of intermediary metabolism. Are there similar rules that make sense of biological diversity and complexity?

    Rules Govern Biological Systems

    As it turns out, the insight I offered my lab mate may well have been prescient.

    The idea that a simple set of principles—rules, if you will—accounts for the complexity and diversity of biological systems may be more widespread than life scientists fully appreciate. At least it appears this way based on work carried out recently by researchers from Duke University.1 These investigators discovered a simple rule that predicts the behavior of mutually beneficial symbiotic relationships (mutualism) in ecosystems. Mutualistic interactions play an important and dominant role in ecosystem stability.

    The Duke University scientists’ accomplishment represents a significant milestone. Lingchong You, one of the study’s authors, points out the difficulty of finding rules that govern all biological systems:

    “In a perfect world, you’d be able to follow a simple set of molecular rules to understand how every biological system operated. But, in reality, it’s difficult to establish rules that encompass the immense diversity and complexity of biological systems. Even when we do establish general rules, it’s still challenging to use them to explain and quantify various physical properties.”2

    Yet, You and his collaborators have done just that for mutualism. Their insight moves biology closer to physics and chemistry where simple rules can account for the physical world. Their work holds the potential to open up new vistas in the life sciences that can lead to a deeper, more fundamental understanding of biological systems.

    In fact, the researchers think that simple rules dictating the operation of biological systems may not be an unusual feature of mutualistic interactions but may apply more broadly. They write, “Beyond establishing another simple rule . . . we also demonstrated that one can purposefully seek an appropriate abstraction level where a simple unifying rule emerges over system diversity.”3

    If the Duke University scientists’ insight generally applies to biological systems, it has interesting theological implications. If biological systems do, indeed, conform to a simple set of rules, it becomes more reasonable to think that a Creator played a role in the origin, history, and design of life.

    I’ll explain how in a moment, but first let’s take a look at some details of the Duke University investigators’ work.

    Mutualism and Ecosystem Stability

    Biological organisms often form symbiotic relationships. When these relationships benefit all of the organisms involved, it is called mutualism. These mutualistic relationships are vital to ecosystems and they directly and indirectly benefit humanity. For example, coral reefs depend on mutualistic interactions between coral and algae. In turn, reefs provide habitats for a diverse ensemble of organisms that support human life and flourishing.

    Unfortunately, mutualistic systems can collapse when one or more of the partners experiences stress or disappears from the ecosystem. A disruption in a relationship can lead to the loss of other members of the ecosystem, thereby altering the ecosystem’s composition and opening up niches for invading organisms. Sadly, this type of collapse is happening in coral reefs around the world today.

    Mutualism Can Be Explained by a Simple Rule

    To gain insight into the rules that dictate ecosystem stability and predict collapse (due to a loss of mutualistic relationships), the Duke University researchers sought to develop a framework that would allow them to determine the outcome of mutualistic interactions. For the predictive framework, the scientists wrote 52 mathematical equations, each one specifically describing one of the various forms of mutualism. These equations were based on a simple biological logic; namely, mutualism consists of two or more populations of organisms that produce a benefit (B) for all the organisms that reduces the stress (S) they experience at a cost (C).

    Mathematical analysis of these equations allowed the researchers to discover a simple inequality that governs the transition from coexistence to collapse. As it turns out, mutualistic interactions remain stable when B > S, and they collapse when this inequality is not observed. Though intuitive, it is still remarkable that this simple relationship dictates the behavior of all types of mutualism.

    The researchers learned that determining the value of S is relatively straightforward. On the other hand, quantifying B proves to be a challenge due to the large number of variables such as temperature, nutrient availability, genetic variation, etc., that influence mutualistic interactions. To work around this problem, the researchers developed a machine-learning algorithm that could calculate B using the input of a large number of variables.

    This work has obvious importance for ecologists as ecosystems all over the planet face collapse. Beyond that, it has important theological implications when we recognize that a simple mathematical equation governs the behavior of mutualistic relationships among organisms.

    Let me explain.

    The Case for a Creator

    From my vantage point, one of the most intriguing aspects of our universe is its intelligibility and our capacity as human beings to make sense of the world around us—quite often, through the use of simple rules we have discovered. Along these lines, it is even more remarkable that the universe and its phenomena can be described using mathematical relationships, which reflects an underlying rationale to the universe itself.

    For most of the history of science, the discovery and exploration of the mathematical nature of the universe has been confined to physics and, to a lesser extent, chemistry. Because of the complexity and diversity of biological systems, many people working in the life sciences have questioned if simple mathematical rules exist in biology and could ever be discovered.

    But the discovery of a simple rule that predicts the behavior of mutualistic relationships in ecosystems suggests that mathematical relationships do describe and govern biological phenomena. And, as the researchers point out, their discovery may turn out to be the rule rather than the exception.

    From my perspective, a universe governed by mathematical relationships suggests that a deep, underlying rationale undergirds nature, which is precisely what I would expect if a Mind was behind the universe. To put it differently, if a Creator was responsible for the universe, as a Christian, I would expect that mathematical relationships would define the universe’s structure and function. In like manner, if the origin and design of living systems originated from a Creator, it would make sense that biological systems would possess an underlying mathematical structure as well—though it might be hard for us to discern these relationships because of the systems’ complexity.

    blog__inline--simple-biological-rules-affirm-creation

    Figure: The Mathematical Universe. Image credit: Shutterstock.

    The mathematical structure of the universe—and maybe even of biology—makes the world around us intelligible. And intelligibility is precisely what we would expect if the universe and everything in it were the products of a Creator—one who desired to make himself known to us through the creation (Romans 1:20). It is also what we would expect if human beings were made in God’s image (as Scripture describes), with the capacity to discern God’s handiwork in the world around us.

    A Case against Materialism

    But what if humans—including our minds—were cobbled together by evolutionary processes? Why would we expect human beings to be capable of making sense of the world around us? For that matter, why would we expect the universe—including the biological realm—to adhere to mathematical relationships?

    In other words, the mathematical undergirding of nature fits better in a theistic conception of reality than one rooted in materialism. And toward that end, the discovery by the Duke University investigators points to God’s role in the origin and design of life.

    Is There a Biological Anthropic Principle?

    As the Duke University scientists show, the discovery of a simple mathematical relationship describing the behavior of mutualistic interactions in ecosystems suggests that these types of relationships may be more commonplace than most life scientists thought or imagined. (See Biochemical Anthropic Principle in the Resources section.)

    This discovery also suggests that a cornerstone feature of ecosystems—mutualistic relationships—is not the haphazard product of evolutionary history. Instead, scientists observe a process fundamentally dictated and constrained by the laws of nature as revealed in the simple mathematical rule that describes the behavior of these systems. We can infer that mutualism within ecosystems may not be the outworking of chance events—the consequence of a historically contingent evolutionary process. Rather, these relationships appear to be fundamentally prescribed by the design of the universe. In other words, mutualism in ecosystems is inevitable in a universe like ours.

    For me, it is eerie to think that mutualism, which appears to be specified by the laws of nature, is precisely what is needed to maintain stable ecosystems. The universe appears to be structured in a just-right way so that stable ecosystems result. If the universe was any other way, then mutualism wouldn’t exist nor would ecosystems.

    One way to interpret this “coincidence” is to view it as evidence that our universe has been designed for a purpose. And purpose must come from a Mind—namely, God.

    Resources

    The Argument from Math and Beauty

    Designed for Discovery

    The Biochemical Anthropic Principle

    The Design of Intermediary Metabolism

    Endnotes
    1. Feilun Wu et al., “A Unifying Framework for Interpreting and Predicting Mutualistic Systems, Nature Communications 10 (2019): 242, doi:/10.1038/s41467-018-08188-5.
    2. Duke University, “Simple Rules Predict and Explain Biological Mutualism,” ScienceDaily (January 16, 2019), https://www.sciencedaily.com/releases/2019/01/190116110941.htm.
    3. Wu et al., “A Unifying Framework.”

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